I have a similar problem

th fro information

Moving folders does not work in Unity 5.4. Moving a folder causes p4 to check out the corresponding files but it does not add the files in the new location as expected and does not remove the files in the old location.

Expected: Moving a file/folder should,
Mark old files for delete
Mark new files as Add

I'd like to point out that this is fully supported by P4Connect, but I'd much rather use the Unity Perforce integration because they respect they server type map and the icons are easier to see.

Not being able to move folders is not only a deal breaking feature, it gets your project into a completely messed up and invalid state.

A workaround for this in the meantime is to just do the folder moves via P4V.

Note: You should probably have the 'Rmdir' option enabled in your Workspace for the old folders to be automatically cleaned up from your Workspace. I have seen cases where even this does not work automatically, however, so in that case you should delete those empty folders manually through Unity and ensure any orphaned meta data be marked for delete in Perforce.