You really have to pay attention with Beyond Compare that you don't over-write lines with partial changes for mods. Typical example is when we add a column to a database table for a mod then add that column to our query by tagging it on the end. Beyond Compare will show it's different from the unchanged files, but unless you scroll all the way to the right to see what the change is you're going to over-write the change if you just copy over it. Upgrading is do-able with BC, it just takes a while...

New upgrade, new method

2 times beyondcompare open.

One with original 7.2 with my 7.2 to find all the hacks
One with my 7.2 and a fresh new 7.2.2 to apply the hacks back again.

Been there several times; I find it a nice way to update with hacks quickly... Then again, I like installing everything manually sometimes... call it OC