You chose to upgrade her on her own. The instant you do that, she is no longer travelling with you for these purposes because you've changed the cabin in which she's travelling while you and your wife are staying put. If you wanted to ensure that you could keep your Silver benefit of free pre-allocation of seats for those who would not be entitled to do so on their own, you could have refrained from upgrading her on her own and waited until there were three award seats and you could all upgrade at the same time and stay on the same booking. Pros and cons to both routes; these are choices we all have to make sometimes.

The same would have applied if you changed her return travel date - she would no longer be travelling with you for these purposes on any of the sectors because she would then also have a separate booking.

You might well find a sympathetic agent who would do something for you. But (as LTN Phobia says), BA wouldn't help a Gold in your situation, let alone a Silver. Many of us have "been there, done that", including paying BA the extra money.I'm sure we all understand the OP's frustration at finding an unwanted (and possibly unforeseen) consequence of something that they were doing for the benefit of someone else.

But if, hypothetically, at the time of booking there had been one U class seat and the OP had decided to book the mother-in-law into CW using that for a UuA, and then made a separate booking for himself and his wife in WT+, it would have been exactly the same position as now. What makes the current request more reasonable? But we all know exactly what the policy is if two separate bookings had been made from the outset. Neither a Gold nor a Silver can expect to escape that, frustrating though that may be.