That's a good question. p. 88 of Strategic Operations only notes that engine-based recharging can demand fuel for both the recharging activity and station keeping. It doesn't address WarShips under thrust, but probably should.
[update] Apparently, there is canon that indicates charging under thrust can occur:
"The Invisible Truth hot-loads its core while trying to make it to a jump point in Dawn of the Jihad p91. P90 mentions they are at 1.5g acceleration at the time."
"Bred for War has Ulric bringing the Wolf fleet slowly into Butler. Not so that Vlad can do assault calculations, but rather so they can hot-load the KF's drives and then jump on to Wotan."
(Thank you, Chris, for spotting those references.)
