Hello Sebastian,
please check your emails, I have answered via the ticket system.
Actually, you must open/save/modify, also work with your R files via the Boxcryptor drive.
Point your R editor to the Boxcryptor drive when opening/saving.
BTW: the .bc extension is added by Boxcryptor to each encrypted file and these files are only on the "Cloud-side".
Best regards,
Yasmin