Some companies really do want to a/b test their shopping cart to death, and have 40 iterations of their logo with roundtable meetings in between, and that stuff can genuinely take many man months and in the case of the a/b testing might even be time and money well spent. I'm sure some of the agency's regular clients spend $400k on getting e-commerce sites which are only a bit more complex overhauled and think they'll see value from it
But 46k is definitely unreasonable for something you've estimated at 7k, and 38 billable hours to refactor a Bootstrap template for a minimalist website with about 10 pages doesn't sound like efficient work.
Dont joke about untangling Bootstrap from your css architecture, I’ve seen that take 6 months to get out from.
And whilst I'm sure there are complex apps and huge sites which are horrendously sensitive to untangling Bootstrap especially where pixel perfect preservation is required, we're talking about implementing three brand new pages of standard layouts plus a handful more black-on-white text pages with existing standard layouts and the new header, font and button carried over. Implementing that in 38 hours is not fast work.