Yesterday we found a way to solve the issue.
When I created a branch, I chose the option "Create branch from tagged version". Apparently this causes the error mentioned above.
When a co-worker created a new branch using the option "Create branch from main line" and then selected the revision that matched the tagged version I selected, we were able to merge fixes from that branch to the main line without errors.
So my guess is that this is a bug in Mendix, either in the Modeler or in version control in the Mendix cloud.
Could it be that the start revision was nog in 5.16.1 but in another version? Did you try creating a branch from that revision and try opening it? That would give you a clue about the version that seems to be missing from the machine that does the merge.