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With the onset of Workflow Comparisons in V2021.3, it only seems natural to me that the next step would be a method of handling those changes. Maybe have some clickable dropdowns on the changed tools that have a few options as to what you'd like to do about them. I think the options to start off with would be "Apply this change to that workflow" and "Apply the other workflow's change to this one" along with the "Apply all of this workflow's changes to that one" and "Apply all of that workflow's changes to this one" somewhere in the header.
I know that I will occasionally get a request to change a workflow while I'm already in the middle of making a change to it or am waiting on approval for a change I've made and am hoping to implement. The current version control system on Server does not make it easy to implement multiple changes that may need to be implemented in an order other than the one in which they were started. The current process seems to be to merge them later by going through the whole process of selectively copying the changed tools and pasting/replacing them or otherwise manually modifying the tools to make them match.
Likewise, implementing the version merging proposed here will allow versioning strategies more akin to branches in git. One could more-or-less maintain two streams of changes until they were both complete and merge or productionize them as they're complete and ready.