There is plenty of reporting out there that indicates William is keenly aware of the impact of being seen with or publicly associating with anyone who has brought dishonor to the monarchy. Before these last two rounds of revelations about Andrew (in Oct/Nov and now), it seemed like he was inclined to have Eugenie & Beatrice acting in a similar support role capacity as Peter and Zara/Mike - showing up at the Garden Parties to mix & mingle - possibly a bit more for a few years until George, Charlotte & Louis were old enough to step into a more public role.
After the Oct/Nov revelations, the reports I was reading & hearing regarding Bea & Eug were that he wanted a thorough investigation of their finances & bank accounts to ensure there wasn't anything questionable - not so much because he believed they were necessarily complicit but because he didn't trust Andrew & Sarah to not have used & convinced their daughters that these sort of things were all perfectly normal, fine & legal. Who knows what came of that or whether their views have changed on doing a thorough investigation of everything their parents ever told them was a-okay and fine.
They were both still fairly young - early 20s if not younger - when Sarah & Andrew were having them escort business partners of Epstein around Buckingham Palace. Given the close relationship they've always had with their parents, I can cut them a degree of slack for going along with those requests or not necessarily realizing just how sketchy these financial transactions were. What needs to be known now is at what point did they become aware enough to put an end to all that?
That's the real issue for both Beatrice & Eugenie. Just how recent is their exposure & intentional was their involvement with whatever shady or illegal shenanigans their parents got themselves up to? At this point in time, there just isn't enough information to know the answers to those questions and until those answers are known, they cannot be involved with the public duties of the monarchy because the public does have every right to ask those uncomfortable questions. And if they don't want to open their own records & finances up to investigation by either King Charles or the Prince of Wales, then the only option is to sideline them entirely.
That's not the same as cutting them out of the family - and I haven't read or seen any reliable reporting that indicates either Charles or William want to do anything so drastic, but there are ways of managing public optics even at private, family gatherings, that would exclude Bea & Eug from the public eye and we may see that play out in coming months.