Removing the UDFs manually using the alter table command is not recommended and will not help you actually.
I believe I have seen code on internet which will take input of the UDFs you want to delete and will do all the work for you of deleting the UDFs and its references.
But since you have already rolled back the sandbox, use the code to delete the UDFs and it probably should remove all the references; if not, you might have to modify the code.
After you delete the UDFs through code, you will have to take the export of USER.xml and remove all the references of the UDFs and import it back.
This should solve your issue.
If this does not resolve your issue, please check you have entries of the UDFs in the following tables:
c. USR (per your statement, you should not have any columns in this table)
Ref : Oracle Docs/Forums.