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modules.conf~ might have been created as a backup. Compare the 2 files and see. Otherwise, the standard/normal one is modules.conf and you should create a backup from it:
cp modules.conf modules.conf.old
Quite a few apps create backups automatically, vim, kate, and a few others. They rename the original with the tilde at the end:
file~
This is linux saving yer butt in case you do something dumb (which we all have...)
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