Pretty easy to explain. I changed some files in my custom sides and now when I munge the rep or cis folder nothing changes.
I did a manual clean and I munged everything that I needed to but the game crashed and when I checked the data_***/LVL_PC/SIDE no .lvl files were there, no files at all actually.
The ***.lvl file showed up in the LVL_PC folder though
Any ideas why this is happening?

Maybe you did an manuel clean before, too and deleted the build/side/rep/munge.bat

Just checked the munge file is still there:
build/sides/rep

The only files that were deleted in the sides folders were ones in:
build/sides/rep/munged/pc

Download and install this. See if it helps. (Read its Read Me for further info on it)
http://www.gamefront.com/files/13892962/munge_fix.zip

Credit goes to the person who made it.

No readme came with it?
haha I have no idea what to do with it

This is why it's a good idea to post links in their original context:

[b][color=#FF8000]The FAQ / Everything You Need Thread Version 2.0[/color][/b] wrote:...
Question #7 - I'm using Vista or Windows 7 and Visual Munge is not working properly, it is munging too fast so what's wrong?
Answer - Try THIS workaround to get it working properly.
...

Well it does seem that I already installed that patch previously so that I could mod in the first place.
I ran it as the instructions said anyway and I know on the post it says that already created maps will not be affected.
So my problem still remains.
The sides were running just peachy before my last manual clean and now no new .lvl files are being created in the data_***/LVL_PC/SIDE folder and replacing it with my back up files will only give me the older version of my sides back.

did you follow the tut on how to add new sides exactly?

Custom sides were working perfectly fine. So, yes, yes I did.
For whatever reason these .lvl files aren't being produced through munging anymore which explains why new changes to my custom sides were not working.

try copying the munger from somewhere else maybe.

That didn't do it either.

what exactly did you do between the time it worked and the time it didn't.

I replaced the Battledroid skin tried to munge but no change appeared in game.
So I tried editing several other skins and they also didn't appear in the game.
Then I changed some msh files around and those changes did not apply either.
So i did a manual clean to try and fix everything and that's when I noticed the .lvl files missing.
Even with these files missing when I run the map the sides will load, just unchanged.
Interesting development though, I copied my sides file to a different map, munged them there, ran that map and the sides changes worked.
Copied the .lvl files for the sides and placed them in the original map, munged, ran the map and they didn't apply.

what was the last working operation completed?

You know I found a work around for it.
Created a brand new world, copied the sides, worked fine.
I'll just copy over the world files to get the rest of my map back and try not to mess up again.
Thank you for your time everyone!

can you add [solved] to your thread name??

it seams something in your build folder was broken.

Well the problem itself was never really solved I just decided to start over and copy the sides folder.
But sure, I'll add solved to the thread name.