First Take a Profile Back Up and Remove/Uninstall the Firefox Nightly and Transfer your profile data's to new profile.

Profile Backup and Restore

• http://kb.mozillazine.org/Profile_backup
• https://support.mozilla.org/en-US/kb/back-and-restore-information-firefox-profiles
• http://kb.mozillazine.org/Transferring_data_to_a_new_profile_-_Firefox

Make sure the "Remove my Firefox personal data and customizations" is Not checked when you uninstall Firefox on Windows.

Why is nightly even messing with my Firefox profile? It's a separate program isn't it?

Nightly is still Firefox in early Alpha basically and it does not create its own Profile. It is not a separate application like Thunderbird and SeaMonkey are.

There has been some debates whether the Nightly channel development builds of Firefox should create a new Profile on start or to use the last one used unless the user starts with the ProfileManager to use a different one from the one used with Release. Technically users should not use Nightlies unless they at least know the basics of separate installs and using separate Profiles for them.

There are four main channels of Firefox development. Release then the three for testing being Beta (27.0b2 currently), Aurora(28.0a2) and Nightly(29.0a1). The Nightly and even Aurora get checkins pretty much everyday so they get a update each of those days.