This was a feature of YNAB 4, Chimi, which many users (including me!) are still using. In that, you could choose whether a category with a negative balance (like Job Expenses before they're reimbursed) would be taken off your 'Available to Budget' amount (which in fairness, you haven't actually got the money so it isn't available to budget) or whether you could select to have the debt just roll forward within its own category.
It relates to another concept that nYNAB doesn't have, which is 'income available this month' and 'income available next month'. Let's say it's 15th Jan and I have -£100 of Job Expenses. I get paid my salary of £1000 and I say that this income should be available to budget next month, so the January budget ignores it and the February budget says 'thanks very much, I'll have a grand'.
If I don't 'turn the arrow to the right', the Feb budget will actually be £900, because it's the £1000 I got minus the 'overspend' in my Job Expenses category.
If I do turn it to the right, my available to budget stays at £1000, but my Job Expenses category shows a -£100 total until those expenses are reimbursed.
You would also have handled credit card debt the same way, so that the debt was 'quarantined' and only affected its own category total. Otherwise let's say I had a card with a pre-existing debt of £2000 on it, my available to budget would always be -£1000 after I'd been paid.
There are various different ways you can try to frig this in nYNAB but I prefer it old skool. God knows what I'm going to do when YNAB 4 finally breaks, probably move off YNAB completely.