This error must have been there before the upgrade, but you are just now noticing them
There are various other options for similar functionality:
Dynamix File Manager plugin. This is likely to be a standard part of a future Unraid release although at the moment it is a plugin you have to install.
The 'mc' (Midnight Commander) from a console session for a character based 'pseudo' GUI. This ships as standard with Unraid and has for a long time.
Do it yourself from a console session using Linux commands. A lot less user friendly and error prone if you are not used to the Linux command line.
At the end of the day you are going to have to manually move files from one folder to another so you can eliminate folders with the same name but different case The error arises due to the fact that Linux file/folder names are case sensitive whereas SMB is not.