Whenever the battery is disconnected for more than about 5-10 minutes and/or an ECM Calibration Update is performed the vehicle will default to stored values. In other words, the vehicle loses its "learned values" memory and resets to factory default. So what you may experience is rough idle, sluggish acceleration, and slightly odd feeling shifting for a 100miles or so until the vehicle gets its head back on straight.
Typically I like to leave the vehicle in the stall for about 5-10 minutes at idle with no loads on (no A/C, lights, radio, ect.) to have it re-learn idle properly. Then inform the customer that they may experience some slight performance issues until it relearns itself.
You can always force this reset by disconnecting the battery for about 10minutes. I do recommend you let the vehicle idle for about 5-10 minutes with no loads and then drive it a good 20 miles or so afterwards. It will still take a few drive cycles to relearn itself completely though.
Also another point is that if the MAF and/or Throttle body are dirty, when the vehicle tries to relearn itself, it may not learn proper values as the dirty MAF and Throttle Body can skew the sensors which the ECM uses to calibrate itself.