Not unless you do something horrendously wrong - the software has safety measures built in to prevent something bad from happening.

If you're worried, and want to keep a backup of your mod installation, consider using the Restore Points feature (Settings -> Utilities -> Restore Points)

Restore Points allow you to create an "as is" snapshot of your entire installation, which is stored in a safe location of your choice. This Restore Point can then be used to bring back your installation to the exact state it was in during the creation of the snapshot.