This is how i proceeded:
1. I made a clean install of SFCOP from CD (2500)
2. I generated a list of folders and files, and their respectives checksums, using a tool.
3. Installed 2552 patch
4. Installed 2561 HD patch
5. Added a gamespy fix, and some little tweaks, on StartFleetOP.exe, sprites.q3 and offsets.txt (2562)
6. Generated another list of folders and files and their respectives checksums.
7. Used a tool to compare the 2 lists and produce the patch.
Resuming:
patch = 2562 - 2500 or 2562 = 2500 + patch