I recently migrated to a new (er) MacBook Pro running Catalina 10.15.7. For full disclosure, I did the Migration Assistant to get my old files and settings and then moved my user directory to another disk. As such my home directory is now /Volumes/UserData/xxxxxxx I don't know if that's part of the problem or not. Other apps don't have any problems.
The problem with SQL*Developer is that when I try to open a folder that I created AFTER the migration to the new system, it can't see it - that is the folder does not show up in the open dialog box list of folders. But it can see (and open) ones that were there BEFORE the migration. Other apps such as TextEdit, BBEdit, Finder can see the folder and open it and any files it contains. If I navigate the directory tree in Terminal, iTerm and Royal TSX I also see the files.
I've looked at the file attributes using xattr and the folder in question has none. I've looked at ACL entries using ls -ale and it also has none. Other folders that I can see and open with SQL*Developer also have none. But some do so it seems that is probably not the culprit. I suspect something with Java but I haven't found anything online that points to where it might be. I am using Java JRE 1.8.0_333 and have been for a while. It did not have this problem before migrating to the new system.