>Some source control programs allow you to "merge" those changes into the two branches, but everyone I've ever talked to...and they've used many different source control tools...has said it was far easier to manually make the changes than to try to do the automated merge.

Quotation marks are fully deserved. I had only one case when the merge did right - and that was a fairly straightforward .prg with a minimal difference between the versions. For anything else, I'd use the merge utility (and I've tried a few) to locate the differences, and apply a much stronger tool to reconcile them: the keyboard.