Having just done this:
1) Downloaded AIWar5035.zip
2) Unzipped it
3) Copied the code .dll into the two spots inside the unzipped structure (one is windows, one is mac, exact same dll since mono is cross-platform)
4) svn-diff between 5.035 and head revision, select all inside the RuntimeData directory, export to RuntimeData directory of unzipped structure
5) re-zip the structure, name it AIWar5036.zip
6) upload AIWar5036.zip
7) change first line in the updates .xml file to say B5036 instead of B5035
delete AIWar5035.zip from the server
Alternatively I could just start at step three with an empty structure instead of the unzipped structure from before, and that would result in an actual increase in the number of update "steps" from the previous official to the next.
The main decision point is the size of the zip files. If there's been a ton of new art, or music, or whatever added then the zip can get kind of big. If only the code has changed it's pretty small (but not inconsiderable, the .dll is kinda big as .dll's go). And if we keep doing rollups like what I described it keeps getting bigger. Once it gets big, we do the next one as a non-rollup.