Basically - the manuals work like thus:

If the item you're going to farm one a single hit, will give you 200 exp, then you'll net 300exp back. Now, if you get HQ exp or chain exp, this is added on to the base, but doesn't affect how much you get as a return from the manual, so - the manual will give you up to 40k exp based off the original 200 exp from that item. So, using 200 exp as a base, that means you can farm 200 of those items for 200 exp + plus manual + chain + HQ bonus before the manual will run out.

So, if you've got rested and you HQ a LOT and you always get chains, the manual will appear to run out well after the 40k exp you initial thought you'd get.