While browsing a Jazz Jackrabbit 2 CC' 99 Disk I found this:

I Wondered what this patch could be...
I Tried replace from the folder to TSF, it didn't work and after I had vision that the patch could be.
I Think the patch is a minor update of JJ2 CC99.

If you have the copy you can research little.

Hmm... Well, I don't know too much about the details of CC99 and HH98, but perhaps it's the 1.23 patch so that you can put the CC99 levels in JJ2(Assuming that the CC99 levels are just the HH98 levels running from within the 1.24x engine).
By the way, I think you've got a broken image in your post.

That "patch.bat" file, when run, copies "Capture3.j2l", "Jazz2.exe" and "Race1.j2l" to "C:\Games\Jazz2 Xmas99". So apparently it expects you to have CC99 already installed in "C:\Games\Jazz2 Xmas99", but it changes the Capture3 and Race1 levels, and something about the game's executable file. What the differences are as compared to the original versions of these files? No idea.

Ah, perhaps it upgrades Holiday Hare '98 to the 1.24 engine, and makes it become CC99?

Proceeding from pretty faint memory here, but did CC99 maybe come with its own CTF and race level/s? The patch could be replacing the next level settings on race1 and capture3 to point to the CC99-exclusive levels. And the .exe change... probably adding those same levels to the internal list of levels that don't show up in the Home-Cooked Levels list/can't be played through command line?

I Hate this is infamous version. Almost all Utilities does not work on this version. This is my favorite version. The worst part? You can't go on normal 1.24 servers.

And why Epic does not sell these games? An adult can got licenses and sell copies on the Internet would be a great idea. That was a EPIC game, like Shenmue by Sega didn't wanted to release it for PC or other modern consoles.

Hmm, I got the 'big box' version of CC99 and it didn't came with this patch.

I played and experimented a lot with CC99 over the past, so I've send you a PM and hope to try it for myself to see if I can find any differences, especially in the exe.

Okay. Got the patch and tested out some non-technical stuff to see what's changed. Here are my findings:

Jazz2.exe
I only found one change in the exe, one that fixes the local splitscreen multiplayer in the menu. Their lines were, besides Treasure Hunt, greyed out and unselectable. This patch however, still has those lines greyed out but they are selectable now.. Thus Co-Op, Battle, and CTF will now work locally. lol yippee. Strangely enough, CC99 had another similar bug which made Treasure Hunt greyed out and unselectable in the network/internet Host Server menu, and this patch doesn't even fix that. How sloppy.

Capture3 and Race1
These level files only have their Next Level setting changed. Capture3 will point to Capture1 instead of 4, and Race1 will point back to itself instead of Race2 as CC99 didn't came with any more Race levels. Strangely but nothing new, the default levels for hosting a server are CC99's exclusive MP levels, which are xmbattle1.j2l for Battle and XC-Frightni.j2l for CTF (that's non-exclusive user level Fright Night CTF).

Also, I don't know why but using this patch will break existing savefiles, resulting in either a glitched level (no bullets, etc) or an Access Violation Error. Probably due to memory locations being in a different place or something, I'm not too technical on that.

So that's it for this mystery patch! Basically, all it does is fixing local splitscreen multiplayer and preventing next level not found errors in 2 MP levels.