Yeah basically during the whole VE table tuning process. You ALWAYS have your MAF disconnected. When scanning, flashing, etc.
If you connect your MAF back on, the PCM will not use the VE table and the whole point of the process is lost.
This is the only time you want to have the MAF unplugged during the tuning process. After that, you never disconnect it again.
BTW, I would skip the VE tunning.