I believe the MergeView editor has a bug related to virtualization. Based on how the content is virtualized, multiple mergeSpacers can start pushing the content on one document and make the 2 documents out of sync.
It’s a bit hard to tell what is going on in the video above. After modifying the background color of cm-mergeSpacer you can start seeing that the content jumps around whenever a spacer is introduced or removed.
I’ve put together a Gist with 2 documents for repro. Hope this helps!