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One additional thing you could do for the client is to seek out any external links to the alternate domains and see if you can update them so they now link to the main domain. As far as a timeframe, I usually see a time period of two to three months for things to restore back to normal. The earliest changes I've seen have been a month. As long as the new merge is, like you said, for usability reasons also, I imagine it's a great move for people using the website and it was a good thing to do. You may want to beef up the content on the main domain for those terms that dropped in rankings, or try to do some guest blogging related to those keywords so you'll get links back to the main domain.

I can't say for sure with out seeing the sites and making sure I understand your question 100% but it sounds like both of them are hurting their SEO by having so many domains that they want to rank....client b more so than client a. Client A is passing link juice from ClientASite.com to Subpage.com. It's not a huge deal if Client A owns subpage but it's going to make ClientASite.com less competitive from an SEO perspective. Client B - same thing but worse since his clients would purchase multiple services that are SubPages. My question is why are they setup like that? Have you thought about building them both new sites and 301'ing the SubPages to pages on the main URL?