My reply settings changed recently, but I didn't set it

Until very recently, if I replied to an email sent to B while I am working in the A inbox, the message will by default come from the B account. Now, in the last few days, it automatically comes from the A account

What about if you reply to that sender in “All Inboxes” and not directly in that account Inbox ?.

As doing that works for me correctly using the latest eM Client V10.4.4209 for PC & Mac.

See this thread post below from @Olivia_Rust which should explain the problem you are having.