Incremental migration, best practice on Git repo sync to avoid breaking work item links?

[sheltoncj]

I've been doing a cross-organization Azure DevOps to Azure DevOps migration of a project and they are ready for a final cut over. My understanding is that if I clone the source repo into the target project to catch up with all of the changes, it will break all of the existing links from work items. What's the preferred way to avoid this or correct it?
The project is large enough that migration had to occur in several chunks over multiple days, so I don't want to wipe the target project and do it all again.

[MrHinsh]

Please check #996 as I think your answer is there.