You have several options.

First, shut down your current sync account. (Read the rest of the message)

Question: Do you want to have access to your work data on your home system and vice versa?

If yes: On the work system, create a new folder off the root directory and call it; Work or something like that. Then move all bookmarks on the work system into the Work directory. This will keep things separate from your home data and make it easy to remove when you want.

If you don't want your work data on your home system, do not use sync on the work system.

If you want to keep work and home separated then you need to use separate Sync accounts or exclude the bookmarks and history from Sync. If you only have one work computer then don't use Sync at all for work since this isn't needed.

I actually think i just made it worse now. At work I logged out of the Sync account with my personal email and created a new account with my work email. I came home and then proceeded to log into sync with my email address and even though I did what i did at work all of the work bookmarks came back on my personal machine and all my personal bookmarks disappeared. What do I do to get my bookmarks back? the recently bookmarked are still there but everything else is missing.

Make sure you used the correct e-mails home or work.

Did you create a new sync account? home and work?

Firefox keeps backup of the bookmarks in the bookmarkbackups folder, so restoring the bookmarks shouldn't be a problem.

• Bookmarks -> Show All Bookmarks -> Import & Backup -> Restore
• https://support.mozilla.org/en-US/kb/restore-bookmarks-from-backup-or-move-them

If you disconnect the work computer then this still leaves its data on the Sync server. With such major changes to the Sync account it might be a good idea to change the password of the Sync account to reset all data stored on the Sync server.