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.
You didn't say how much you charged for that job, so it is impossible to give assessment there. But it is almost certain you charged way too low.
From what I can gather, you provided a lot of services there. It's not so much the designing and the 3D model that counts, but all the services you describe, that are really, really valuable. Because you provide a total package and one that is facing regulatore/legal.
Two years of site visits alone would amount to ~50 trips. This alone would be worth 20k at least, since you also are bound for that time and cannot leave town etc. Hard to say without further details…
Edit: Basically it feels like I currently do an order of magnitude more work for the same money.
Agencies and Consultings aren’t simply overcharging. They’re also weaponising incompetence and inefficiency so they can bill more hours.