Mds delete - now have communication error codes

Greetings!
I just bought a 2005 Magnum. Drove it about 200 miles and decided to turn off MDS (it was driving me nuts).
I first checked the DIAG codes - no codes.
Read the car, turned off MDS, wrote the car.
Started car and rechecked the codes - communication errors between all modules and no CEL on the dash.
Cleared the codes.
Proceeded to drive it 2300 miles home, and dropped it off at my buddies shop.
On the way home, no AC.
My buddy said that he filled it with refrigerant and the compressor is coming on, but not the fan.
He wants to reflash the whole car with stock tune and see if that fixes it.
My question is this - Does disabling MDS usually cause a communication error?
Thanks in advance for your time and responses!
Tommy Two-Tone

No it shouldn't Mine is disabled over 300,000km

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Originally Posted by Jfraser

No it shouldn't Mine is disabled over 300,000km

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Gotcha, appreciate it! My buddy thinks that there may have been communications issues between the computers before I disabled MDS. I am just surprised I did not see any codes before flashing it.
He is going to have his tuner put the stock tune back on - and then fix the A/C. (the fan is not coming on with the compressor)
I will disable MDS again when I get it back and hopefully no error codes.
Thanks!

I've had a communication error that has been set to permanent and has shown up in my DTC list every time ever since the day I did my cam install and mds delete, though it hasn't seemed to have any kind of troubling effect really...a 0100 code I believe...