Soft coding is stored on the EEPROM. Use boot mode to download the EEPROM .bin file and then you can use tunerpro to edit the soft coding, prior knowledge of the SKC is not needed to change the EEPROM file. Other useful stuff you can do in the EEPROM includes reading the SKC (so you can clone original ECU SKC to another ECU), turn off immobilizer, change the VIN to match car if you have a replacement ECU.   
Be sure to reset the check sums after making any changes to the EEPROM file then you can boot mode flash the updated file back to the ECU. Really helps to have a bench harness (made form old spare ECU harness) to do the boot mode flashing since you need to open the case of the ECU. 

Never needed SKC to change softcoding...SKC only needed for immo to pair to cluster unless it immo 2 which its not needed as it doesnt use one

I thought the SKC was needed because VCDS won't accept the coding, after reading through some forums people were saying a login is needed to perform this...

Everyone starts out somewhere and it's very dissapointing to get replies like this even after avoiding the main forums to not disturb the more technical threads with experienced users.
Where would you suggest me asking this question, if not here?

somebody messed up Eeprom. when doing immo off - maybe wrote some random immodest off Eeprom from other ECU - the best way , revert to original and do immo off as it should be done

This is probably true, however getting it back to original is something I can't do right now, the guy that did my immo off is in a different country, so I kind of have to deal with this mess myself.

He did write something off another ECU I think, because the ecu VIN in vcds doesn't match with my car anymore... I think it's an A4 B6 VIN...

Couldn't I just read this eeprom and correct this coding, then write it back? I know it's more complicated than that and I'm willing to learn, I just need to know it's possible

just so there's not just useless replies like your first one and this one as well, here is how i solved this a year later and never got around to posting it.
The eeprom was corrupted, my flash contained a manual file (tuned file for that exact car) and only the eeprom was coded as an automatic, so your comment saying it doesn't accept coding of something that doesn't exist in flash is funny, I actually checked the VARDEF with WinOLS and my file was as correct as it could be.

Looking back, maybe the coding wasn't being accepted via VCDS, because of the current EEPROM coding not being stored in the VARTAB of the flash.

I did read the eeprom with VAG Commander and made the necessary changes to the file, including changing the VIN because it was from some B6, but couldn't write it back through OBD and I wasn't so good with electronics back then to write to it directly.

Flashing the ori file or reflashing my tune through obd didn't do anything to the eeprom and it stayed coded as an automatic...
...but when I crossflashed a file from a different ECU (TT180 afaik), the eeprom edited itself to the its coding (of the TT file), which was still wrong for my car, however, flashing my tune back finally edited the eeprom back to the correct coding.

This is apparently the easiest way to get this done in this exact situation I was in, if you don't want to open up your ECU or get into boot mode.