I have a strong suspicion of what went wrong.
Mac OS X uses a hybrid GPT + MBR, where the GPT is authoritative and the MBR is not. When using a Hybrid GPT + MBR, you need to make sure that every single tool you use that ever edits partition tables knows how to handle Hybrid GPT + MBR setups correctly. I suspect the partition-splitting you did in Windows only updated the MBR, and the OS X Mountain Lion update saw the discrepancy and "fixed" it by overwriting the "corrupt"/"incorrect" MBR with a new copy of the data from the "authoritative" GPT. So it probably wiped out any information about how you'd split that Windows primary partition into a smaller primary plus an extended.
Without knowing exactly which block your post-split, smaller Windows primary partition ended on, and which block your post-split, Windows extended partition started on, there's no way to fix this. Also, even if you did know those block numbers, if you ran any OS that did a read-write mount of that "recombined" or "larger, no longer split" Windows primary partition, and wrote any data to it, there's a chance it could have overwritten the blocks at the beginning of the post-split extended partition, corrupting that volume and wiping out its records of what files are stored where.
One way to fix this (assuming the directory data structures at the start of the extended partition didn't already get stepped on), would be to read up on GPT and MBR table formats and low-level tools, look at what your GPT and MBR looked like before the Mountain Lion upgrade (assuming you have those tables backed up somewhere, which is somewhat unlikely because a lot of backup software backs up files or partitions, but not the entire disk including the partition table sectors), look at what they look like now, and use the low level tools to repair the damage.
If you do have a sufficiently recent (but pre Mountain Lion upgrade) full-disk backup that includes the partition tables, you might be able to fix this without going to low-level, something like this:
- Back up any work you've done since the Mountain Lion upgrade.
- Test your backups.
- Restore your full-disk backup.
- Test it to make sure your two split partitions show up again and work correctly and have all their data.
- Run a tool to sync your MBR and your GPT, this time taking your MBR as authoritative.
- Test it to make sure everything's still fine.
- Make a full disk backup again.
- Test your backup.
- Install Mountain Lion.
- Test to make sure the Mountain Lion install didn't lose your split volume this time, or cause any other problem.
- Carefully restore the files you backed up in step 1.