Tuneup Deleted Bookmarks

Hello James. 
Thank you for contacting AVG Community Support.
We will check and help you to clarify it. 
AVG Tuneup will only clear the download and Browsing history. It will not delete the Bookmarks. If you think AVG Tuneup causing this issue, we request you create a new bookmark and scan the PC using AVG Tuneup and check whether you can access the new one. 
Keep us updated.

I just ran a clean-up with Tuneup but it has deleted all of my bookmarks on Firefox. Can anything be done or are they lost?

Hello James. 
Thank you for contacting AVG Community Support.
We will check and help you to clarify it. 
AVG Tuneup will only clear the download and Browsing history. It will not delete the Bookmarks. If you think AVG Tuneup causing this issue, we request you create a new bookmark and scan the PC using AVG Tuneup and check whether you can access the new one. 
Keep us updated.