I was thinking of exporting all, delete the bad ones, delete the DB and reimport all.
But @attah proposal is probably simpler.
You could also search what is different between SIM and normal contacts into the DB and change it to make the contacts form the sim deletable.
The DB is in /home/defaultuser/.local/share/system/privileged/Contacts/qtcontacts-sqlite/
And you can e.g. open it with sqlitebrowser through ssh
Make a copy of the files located in this dir first!