I try to copy a new folder over an old one with the same name. I want every file of the new folder to replace the file of the old folder with the same name, if exists. Instead of this, I get the message:

I have noticed a similar but not identical problem - using spaceFM under iceWM within Luddite an attempt to cut/paste one forder or selection of folders into another the 'paste' option is greyed out and unavailable. I thought it might be normal for spaceFM ? I have seen the same under Berta Caceres although can't prove that as I went back to Luddite for a while.

Likely your problem is the fact that both folders have the exact same name, change one name slightly, & try again.

Or, you could try this command from a terminal. Edit: You may need to use sudo, or the root account, if you don't 'own' the directory.

Reading post #1 reminded me of a known spacefm bug (reported to github issue tracker against v1.0.5).
The bug is specific to files residing on a FAT32 target. Even sudo/root may be unable to perform a directory overwrite (or delete) operation.

As for rox-filer, idunno (post #1 lacks sufficient detail)