On 4 Sep 2018, at 18.45, Rick Romero <rick@havokmon.com> wrote:

https://imapsync.lamiral.info/FAQ.d/FAQ.Duplicates.txt

Seems to use UIDs so that 'data' isn't lost.

No it does not. This is different thing. This is about managing duplicates on multiple syncs.
Imapsync seems to keep track of UID -> MAIL mapping for server A and UID -> MAIL mapping for server B so that on multiple runs it does not sync the same messages again. However it does not use the same UID -> MAIL for server B as is originally on server A. And that is the problem.

Sami