IF Folder 1 and folder 1 are in the same area of a file structure will Endpoint protection view it the same way as Windows does?
Symantec Endpoint Protection 14.2 RU1
Windows 10 - 1809 and New Features in SEP 14.2 RU1
If the feature is not enabled to use case sensitive folders, it will not impact the folders being checked by SEP.
Basic Compatibility in the context of the 14.x product line indicates that there is Full Support for all Windows Features except for case-sensitivity. Case-sensitivity support begins in Symantec Endpoint Protection 14.2 MP1.