This is a bug in the 8.13.* versions of Mendix Studio Pro. You can fix it by upgrading to 8.14.1 or above.
”We fixed an issue that caused a crash when committing to an app project after renaming or deleting a module. (Tickets 69006, 107979)”
https://docs.mendix.com/releasenotes/studio-pro/8.14
if you don’t want to update to that version of Mendix Studio Pro yet you can re-create the two modules you deleted (making them empty should be fine but they have to have the exact same name) and then you should be able to commit to the team server.