Answer
This question is particularly important because continued accrual of unlawful presence during removal proceedings can trigger the three-year or ten-year bars, severely limiting future immigration options.
General Rule: Yes, Unlawful Presence Continues
Once removal proceedings commence (i.e., when the NTA is filed with the immigration court), unlawful presence generally continues to accrue while you are physically present in the United States. The Board of Immigration Appeals (BIA) has consistently held that the three- and ten-year unlawful presence bars under INA S212(a)(9)(B)(i) continue to run while a noncitizen is in removal proceedings.
This can create a particularly harsh situation where individuals are caught in a Catch-22: they often cannot leave the United States while fighting the removal proceedings (as departure could be deemed an abandonment of their case or trigger an automatic removal order), but staying continues to accumulate unlawful presence, potentially leading to more severe bars.
For more details, read the full blog post: Another Problem for Legal Immigration: NTAs (Removals/Deportation Despite Legal Stay.