Yes, I would say that you can do the update, but I'd still recommend following the backup procedure that I outlined above. I did a quick scan of the changes since then, and there don't appear to be any backward compatibility issues.
The tree structure hasn't changed, so your simplification checker should still work. (That is, of course, without having seen any of the code). There were some significant changes this past summer, but they are mostly to the non-formula MathObjects, and I tried hard to make it all backward compatible.
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List("0, ...")->cmp v. "NONE" bug
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