A workaround is to add the following to the post_install step in ios/Podfile. This way it will be automatically applied when you reinstall dependencies.
# Link headers to fix build on case sensitive file systems
# This will only be executed on case sensitive file systems where "pods" doesn't resolve to "Pods"
unless File.exist? "pods"
# For files, create a symlink with `ln -s`
system('cd Pods/Headers/Public; ln -s Protobuf protobuf')
# For directories, create a symlink with `ln -sfh`
system('cd Pods/Headers/Public; ln -sfh OpenSSL openssl')
# Some cases require more advanced scripting to resolve errors that happened during the installation
# For example some files might end up in the wrong director and need to be manually moved
# Ensure Yoga headers end up in the same directory, and create a symlink to allow other iOS code to import fom lowercase "yoga" directory.
system('cd Pods/Headers/Public; mv `find yoga/*.*` Yoga; rm -rf yoga; ln -sfh Yoga yoga')
# Add a similar step for each dependency with broken headers
end