Long story short, my alternator bit the dust on the highway, red battery light popped on, transmission went into SAFE MODE and I drove 7 miles to my indy who replaced the alternator, all set. After about 50 miles SES light came on, brought it back, he read an "48" code which is the torque converter code, reset the SES and off I went, 50 miles later, SES came on. This time I went out and bought the Barvarian Technic software program / cable so I could do my own diagnostics. The indy told me that his friend said that after a SAFE MODE, a BMW dealer may have to reflash the transmission module but he did not have all he info. Anyways, I read the code and sure enough 048 Torque Converter Slip which I reset, 7 miles later, threw the code again, this time I used the BT activation option and reset the transmission's "adaptive memory". Been 100+ miles now, no SES, life is good.
As a side note, the transmission has always shifted perfectly, tight, crisp shifts and the previous owner said no transmission issues for him... hope this helps anybody else that had the TRANS SAFE light up from a battery issue. A bad indy might tell you to change your transmission or fluid (which I'm doing anyways) or both.
I love the Bavarian Technic software and would recommend it $287 and as close as you can get to the $10,000 BMW software.