Okay, I think you have a few misconceptions on CMC, so let me see if I can help you straighten them out.
First, there are two modes for CMC. There's the Movie Library mode, and then there's the Music Library mode. The Sync for each is completely separate. To sync Movies, you have to be in the Movie Library mode, and to sync Music you have to be in the Music Library mode.
The Settings screen has been unified, so you can configure both Movie and Music Library settings no matter which mode you are in.
It is correct that the Sync icon in the Movie Library disappears when you remove all Movie folders. That has nothing to do with the Music Library Sync.
Maybe you haven't discovered this yet: to reach the Music Library, you need to go UP to the menu icons, and then go UP again, which drops down the Mode Bar, which has a silver brushed metal appearance:

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From there you go right and select the music note, which opens the Music Library. There you will see a similar top menu bar with a Sync Icon. Running this Sync only syncs your music:

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Teddyboy wrote: Mon Aug 05, 2019 9:37 pm
Worse case I would have to re export my movie collection again if it wiped it out.
This is not correct. CMC did not wipe out your movie collection, and you would not have to re-export it. I think you've realized this, because you re-exported from CME, and it didn't fix the issue. Your exported data was never altered by CMC - it always just reads the exported data, but never modifies or deletes it, so it is impossible for CMC to wipe out your movie collection.
Teddyboy wrote: Mon Aug 05, 2019 9:37 pm
Well it did wipe it out and I haven't been able to get it back! I re exported, but the collection refuses to display.
It appears that what has happened is that CMC's SmartSync feature has become confused by you adding/removing/re-adding folders. The SmartSync takes a snapshot of your media folders, and then each time you run a new SmartSync, it makes a new snapshot, compares it to the previous snapshot, and identifies any changes from the previous snapshot. In certain circumstances, like adding/removing/adding folders, the snapshot's get out of sync, and CMC thinks there are no changes. So you removed a folder(s), which ended up removing the titles from CMC's local DB, but then after re-adding the folders you ran another SmartSync, and it's just not seeing any changes, so it's not re-adding the titles.
While the SmartSync feature runs right 99% of the time, it can get confused like this on occasion. The solution is simple, just run a Full Sync.

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The Full Sync ignores the SmartSync snapshot, and instead re-imports all titles and rebuilds the local CMC DB from scratch. This is effectively what you were trying to accomplish by re-exporting everything from CME, but you just needed to run the Full Sync to re-import everything.