I have never removed any definitions manually via the UI. Here’s the timeline.
Installed DT3 on both Macs. Definitely noticed the custom metadata in the preferences because I remember thinking it was cool and I should come back to them.
Set up syncing, got DT To Go as well, added those devices as well. Everything syncing over WEBDAV just fine.
Yesterday, noticed that I didn’t have the custom metadata in the preferences on either machine, don’t know when it disappeared, went looking here. Found a thread from May saying that stopping DT, removing the plist file and restarting it would restore the values. I did that on both machines one at a time. Observed that the problem seemed to be fixed on both machines.
Came back today and the values have been removed again. Both of the plist files are empty again, both sync logs indicate that values were removed as part of the sync from the webDAV location.
So I’ve never removed any values through the UI, but I did remove an empty file from each machine while that copy of DT was stopped, causing them to be replaced with the defaults.
I guess it’s possible that doing the fix that way pushed something to the sync location before the file had been rebuilt? I wouldn’t be surprised; sync is hard. But that wouldn’t explain why I lost the values (on both machines) in the first place.
Hope that helps.