I make it a habit to master-restore, modify (I have some personal mods of my own I tweak from time to time, yes, I'm a bit meticulous), delete old mergedpatch, create new mergedpatch, masterupdate.
Just a note on this -- for everyone because I see a lot of people using merged patches:
Do you use a merged patch? Do you know why you're using one?If the answer is 'no', stop using it. Unfortunately the mentality is going around that a merged patch will just make everything work together hunky dory, but this isn't the case. In fact, in some cases using one has been known to cause CTDs (some mods clearly aren't too happy with the result of the merge).
A merged patch is a useful tool for
specific records of
specific mods. If you're making one with the 'select all mods and hit create merged patch' you could be damaging up, and not improving, your game. Using just an example from MMM and FOOK if you create a merged patch with these mods you are undoing intentional changes in how the mods work together.
There's a reason we made the FOIP patches -- these are painstakingly hand-made 'merged patches' that merge what should be merged, and don't merge what shouldn't. While FO3Edit's merged patch functionality only works on certain record types, these include level lists which MMM and FOOK use extensively. Some lists are
designed to replace eachother, and merging them undoes this work.
There are some very good legitimate uses of the merged patch functionality, but it should be used on select mods only that you
know you need to merge to get the functionality you're after. Otherwise, don't use one, you don't need it and it's possibly hindering and not helping.
I return you to your normal programming...