It seems that you are considering two options:
- Repaint with a lead encapsulating paint (specifically designed to go over lead containing paint and with an additive designed to discourage kids eating it).
- Whole house lead abatement followed by painting with "regular" paint.
I can't imagine that adding a second coat of encapsulating paint would be a recommended practice (since your research hasn't turned up any indication of it being so), however, I can't fathom how it would, in any way be harmful and/or detrimental.
I'm certain that encapsulating paint is going to be significantly more expensive than "regular" paint, but I'm also very confident in stating that it's significantly less expensive than full-house lead abatement followed by a "regular" paint job.
Since lead paint is high on your list of concerns, and you are not (apparently) made of money, I'd recommend...
Actually, after having reread the original question a couple of times, I would recommend having each room tested for lead paint. At this point, you don't know which rooms may have lead paint and which don't.
While a "historic house" will likely have had coats of lead-based paint applied over the years, it's entirely possible that someone in the last 40-50 years has already done remediation in one or more rooms. Lead test kits are readily available at my favorite big-box store for $35 or less (half the price of a single gallon of quality paint) and look like they contain enough testing material to do a huge house.
Once you know how much lead paint you're dealing with, you can make a more educated decision. While full remediation is expensive, doing the two rooms that test positive is much less expensive than the whole house and might just about break even with a full house repaint with lead encapsulating paint.
We now return you to the originally posted answer:
going to with a full coating of encapsulating paint. It seems like the most cost-effective way of dealing with the situation. You could save money by only encapsulating rooms that hadn't been done before, but unless there is a method of testing for prior applications of encapsulating paint (and those methods of testing are less expensive than just painting), it looks like your best option.
I'd also suggest starting and keeping up with a "home maintenance journal" indicating that you have coated all interior/exterior (as applicable) surfaces with the encapsulating paint. That way you remember 30+ years from now, and you'll have a list of things you've done to share with the realtor when you decide to sell so the next person doesn't have to wonder. It could make the sale easier and probably net you a little more profit.