The January 15 deadline was only about the Braves' players' ability to get a bonus and other teams' ability to choose how it was applied. But they can still sign anyone they want between now and July 1. Given the money lost from Santana (and the possibility of more) the ability to float a bonus into 2018 was probably not for the Phillies anyway especially when they could still spend more this year (what they have, plus they could trade for more if they needed to).
Technically the Braves players could still sign with any team but they wouldn't get money. But this is also true if they re-sign with the Braves. It would actually, IMO, look bad if they re-signed with the Braves because that would suggest they had a comfort level with a scout or front office person who is still there, which would in turns suggest that scout or front office person was involved in the violations.