InCopy script to export blank PDF with annotations + Acrobat Quick Action JavaScript to import them into PDF exported from InDesign

Batch Export PDF annotations.jsx

//DESCRIPTION:Export blank PDF with annotations for later import into PDF exported with InDesign

(function () {
    // ============================
    // Export all open documents to PDF
    // - Hides all layers before export (restores afterwards)
    // - Enables "Include notes as annotations" (best-effort across versions)
    // - Exports to the same folder as the document
    // - Forces file names to end with "_annotations.pdf"
    // - Shows a summary of failures at the end
    // ============================

    function getPDFExportFormat() {
        // Be tolerant to naming differences across app versions
        try { if (ExportFormat && ExportFormat.PDF_TYPE !== undefined) return ExportFormat.PDF_TYPE; } catch (e) { }
        // try { if (ExportFormat && ExportFormat.pdfType !== undefined) return ExportFormat.pdfType; } catch (e) { }
        // try { if (ExportFormat && ExportFormat.adobePDF !== undefined) return ExportFormat.adobePDF; } catch (e) { }
        throw new Error("PDF export format is not available in this app/version.");
    }

    function setIncludeNotesAsAnnotations() {
        // Some versions expose different property names; try both.
        var ok = false;
        try { app.layoutPDFExportPreferences.includeNotes = true; ok = true; } catch (e) { }
        // try { app.layoutPDFExportPreferences.includeNotesAsAnnotations = true; ok = true; } catch (e) { }
        return ok;
    }

    function hideAllLayers(doc) {
        var states = [];
        var hadLayers = false;
        try {
            if (doc.layers && doc.layers.length > 0) {
                hadLayers = true;
                for (var i = 0; i < doc.layers.length; i++) {
                    states[i] = doc.layers[i].visible;
                    try { doc.layers[i].visible = false; } catch (e) { }
                }
            }
        } catch (e) { }
        return { hadLayers: hadLayers, states: states };
    }

    function restoreLayerVisibility(doc, snapshot) {
        if (!snapshot || !snapshot.hadLayers) return;
        try {
            for (var i = 0; i < doc.layers.length && i < snapshot.states.length; i++) {
                try { doc.layers[i].visible = snapshot.states[i]; } catch (e) { }
            }
        } catch (e) { }
    }

    // Build "<base>_annotations.pdf" from the document name.
    function annotationsPDFName(name) {
        // Replace the last ".ext" (if any) with "_annotations.pdf"; if no extension, append it.
        return name.replace(/(?:\.[^.]+)?$/, "_annotations.pdf");
    }

    function exportDocumentAsPDF(doc) {
        // 1) Resolve the document's own folder
        var folder = null;
        try { folder = doc.filePath; } catch (e) { }
        if (!folder) {
            throw new Error("Document is not saved (no containing folder).");
        }

        // 2) Build the output name "<doc>_annotations.pdf"
        var pdfFileName = annotationsPDFName(doc.name);
        var pdfFilePath = folder.fsName + "/" + pdfFileName;

        // 3) Hide all layers (restore afterwards)
        var snapshot = hideAllLayers(doc);

        // 4) Ensure "Include notes as annotations" is enabled (best-effort)
        setIncludeNotesAsAnnotations();

        // 5) Export to PDF without showing the dialog
        var fmt = getPDFExportFormat();
        try {
            doc.exportFile(fmt, new File(pdfFilePath), false);
        } finally {
            // Always restore layer visibility even if export fails
            restoreLayerVisibility(doc, snapshot);
        }
    }

    // ============================
    // Run
    // ============================
    if (app.documents.length === 0) {
        alert("No documents are open.");
        return;
    }

    var failures = [];
    var successes = 0;

    for (var i = 0; i < app.documents.length; i++) {
        var doc = app.documents[i];
        try {
            exportDocumentAsPDF(doc);
            successes++;
        } catch (e) {
            failures.push({ name: doc.name, reason: (e && e.message) ? e.message : String(e) });
        }
    }

    // Final summary
    var msg = "Export finished.\n\nSuccesses: " + successes + "\n";
    if (failures.length > 0) {
        msg += "Failures: " + failures.length + "\n\n";
        for (var j = 0; j < failures.length; j++) {
            msg += "• " + failures[j].name + " — " + failures[j].reason + "\n";
        }
    } else {
        msg += "Failures: 0";
    }
    alert(msg);
})();

Import PDF annotations from sidecar PDF.js

/*
 *  ================================================================================
 *  Annotation Importer for Adobe Acrobat Quick Action
 *  ================================================================================
 *
 *  Description:
 *  This script is designed to be used as a step in an Adobe Acrobat Quick Action.
 *  For each document processed by the action, it automatically finds a corresponding
 *  "_annotations.pdf" file, copies all annotations from it, and adds them to the
 *  target document.
 *
 *  Workflow:
 *  1.  For the current document (e.g., "MyFile.pdf"), it constructs the path for a
 *      source document (e.g., "MyFile_annotations.pdf") expected to be in the
 *      same directory.
 *  2.  It opens the source document in the background.
 *  3.  It copies all annotations from the source document.
 *  4.  It closes the source document.
 *  5.  It adds the copied annotations to the target document.
 *  6.  It saves the target document.
 *
 *  Behavior:
 *  - On success, the script is completely silent.
 *  - If the target document already contains annotations, it is skipped and a
 *    message is logged to the console.
 *  - If a source PDF is not found, or if it contains no annotations, an alert
 *    will be displayed for that specific file, and a message is logged to the console.
 *
 *  Usage:
 *  - Create a new Quick Action in Adobe Acrobat.
 *  - Add an "Execute JavaScript" step.
 *  - Paste this entire script into the step's options.
 *  - Run the action on one or more open files.
 *
 */

var targetDoc = this;

// Check if the document is saved, as a path is required.
if (!targetDoc.path) {
    console.println("\n--- Annotation Import Report ---\nFile: Unsaved Document\nStatus: SKIPPED\nReason: Document must be saved first.\n--------------------------------\n");
    app.alert({
        cMsg: "An unsaved document was skipped. Please save it and run the action again.",
        cTitle: "Unsaved Document",
        nIcon: 1 // Error Icon
    });
} else {
    // Safety Check: Skip if the document already has annotations.
    var existingAnnots = targetDoc.getAnnots();
    if (existingAnnots && existingAnnots.length > 0) {
        console.println("\n--- Annotation Import Report ---\nFile: " + targetDoc.documentFileName + "\nStatus: SKIPPED\nReason: Document already contains " + existingAnnots.length + " annotation(s).\n--------------------------------\n");
    } else {
        var suffix = "_annotations";
        var sourcePath = targetDoc.path.replace(/\.pdf$/i, suffix + ".pdf");
        var sourceDoc = null; // Initialize as null

        try {
            sourceDoc = app.openDoc({ cPath: sourcePath });
            // If the line above fails, it jumps to catch, and sourceDoc remains null.

            // Force the script to wait for the document to be fully loaded.
            sourceDoc.syncAnnotScan();

            var annots = sourceDoc.getAnnots();

            if (annots && annots.length > 0) {
                // SUCCESS PATH: Silently process, save, and finish.
                targetDoc.bringToFront();
                for (var i = 0; i < annots.length; i++) {
                    targetDoc.addAnnot(annots[i].getProps());
                }
                targetDoc.saveAs(targetDoc.path);
            } else {
                // FAILURE PATH 1: No annotations found. Show an alert.
                console.println("\n--- Annotation Import Report ---\nFile: " + targetDoc.documentFileName + "\nStatus: FAILED\nReason: Source file contains no annotations.\n--------------------------------\n");
                app.alert({
                    cMsg: "Source file for '" + targetDoc.documentFileName + "' contains no annotations to import.",
                    cTitle: "No Annotations Found",
                    nIcon: 2 // Warning Icon
                });
            }
        } catch (e) {
            // CATCH-ALL ERROR HANDLER
            if (sourceDoc == null) {
                // If sourceDoc is still null, the error came from app.openDoc.
                console.println("\n--- Annotation Import Report ---\nFile: " + targetDoc.documentFileName + "\nStatus: FAILED\nReason: Source file not found.\nPath Checked: " + sourcePath + "\n--------------------------------\n");
                app.alert({
                    cMsg: "Source file not found for '" + targetDoc.documentFileName + "'.\n\nPath checked:\n" + sourcePath,
                    cTitle: "Source Not Found",
                    nIcon: 1 // Error Icon
                });
            } else {
                // If sourceDoc exists, the error happened during processing.
                console.println("\n--- Annotation Import Report ---\nFile: " + targetDoc.documentFileName + "\nStatus: FAILED\nReason: An unexpected error occurred.\nError Details: " + e.toString() + "\n--------------------------------\n");
                app.alert({
                    cMsg: "An unexpected error occurred while processing '" + targetDoc.documentFileName + "'.\n\nError: " + e.toString(),
                    cTitle: "Unexpected Error",
                    nIcon: 1 // Error Icon
                });
            }
        } finally {
            // Final cleanup: ensure the source document is closed if it was opened.
            if (sourceDoc) {
                sourceDoc.closeDoc(true);
            }
        }
    }
}