I assume you control both machines.

If you disconnect the second Firefox from Sync, any action taken in that Firefox will be local only and not synchronized to the first Firefox.

Then... what did you want to do with the bookmarks? Depending on the amount of time between creating the set you wanted and the combined set, Firefox might have created a backup. You could check the Restore menu. Please note that there's no "Undo" for the Restore feature, so if you might want to work with the current set again, make a Backup first. Both procedures are covered in this article:

Restore bookmarks from backup or move them to another computer

Does that get you closer to where you want to be?

Was the initial Sync finished completely?

Syncing bookmarks is done in smaller chunks, so if you have a lot of bookmarks then this can take some time for the first sync to finish.

If the first sync was still in progress when you disconnected Sync then you probably should be cautious with reconnecting to Sync if you want to do this. If you do not want to sync all bookmarks then you need to exclude the bookmarks from syncing on all devices.

There is an undo in the Library (Organize -> Undo) for actions done during the current session to bookmarks, but I don't know if this includes data added via Sync.

From what you say then there is no way that sync "remembers" where what data comes from what machine. I never realized how many bookmarks were work related vs general use. Thank you for your responses. I will now delete all bookmarks from each machine that are not relevant to that machine. Some work involved but I guess I didn't understand sync service.

I think that Sync keeps track of from what device specific data comes to be able to send this data to other devices and not to the original device. Only there is no data cleared on a device if you disconnect Sync. What happens on a next reconnect might not always clear though if you remove specific data from multiple devices. I don't know whether reconnecting in such a case might restore some deleted data.