There was little reason for Atari to believe they could make money from BG3, at least not without waiting a long time and/or suing Interplay for it.
At that point, Interplay owed money to Atari, the IRS, banks, Warner Bros., their own employees, and others. At one point they even had their office locked down for a day and almost got evicted for failing to pay rent. Their stocks were worth pennies, most of their licences had been sold, several divisions were closed or sold, they had little cash, and the company's revenue was down. The fact they couldn't (or wouldn't) even pay a $200k advance was also a strong sign that the ship was sinking.
Interplay also lied to their employees about the loss of the licence, they said it was "an accounting error". If Atari learned about it, that's another red flag added to the list.