Except, Crunch, that the rules say the GM "may allow" the player to buy off a Negative Quality. The rule says nothing about the GM being able to FORCE a player to buy off a NQ, or declaring that one NQ is being swapped out for other NQs. Either of those options is a House Rule.
Thus, a player can pay the principle of the debt down to nothing and then keep the In Debt quality on their sheet, tell the GM "No thanks, I'm fine" when the GM makes them the pay-off offer, and keep making monthly interest payments of a whopping 0¥ for the rest of eternity.
Once again, The Negative Quality "In Debt" is still on the character sheet, and is still ticking away its mechanical effect every month like clockwork. The effect, however, has been rendered moot because 10% of 0¥ is nothing.
If it's still on the sheet, it can still have an affect. What's that, you didn't pay off that 3,000¥ interest rate this month because you paid your debt in full last month? Hmm...must be an issue with our books, guess Mickey isn't that reliable these days, which kneecap do you favor. Heck, errors happen all the time in completely legal businesses today, why wouldn't they in 2070. Likely worse if it's not a legal debt.
To be more technical, if you owe 0¥ how do you pay it? Because if you don't pay it, they may send someone looking for you. This isn't to mention the entire hassle of issues that could crop up just from being associated with whoever you had the debt with personally and the debt becoming favors for silence on the matter.
If the player doesn't want the Quality to affect him, he needs to buy it off which would remove it from his character sheet. An addict that has roleplayed recovery still has to check for addiction till he buys it off, other negative qualities wouldn't be any different. If the player wants to have his debt removed, he needs to buy it off. If he doesn't want it removed, and pays it off, the GM should be able to still make it stick.
-Debtor sold the claim, but took the last payment and bolted, character is still on the hook.
-Debtor "lost" record of last payment, character is still on the hook.
-Error causes characters debt to have been more than it originally was, character is still on the hook.
A few examples of numerous ways it can still pop up if it isn't bought off. Now, you could claim that it's a "house rule" to keep the quality in play, but I'd like to point out that it never states you can actually remove the debt or pay it completely off without getting rid of the quality.
What would be a good replacement? While specifics depend upon the table, one should be able to state some broad guidelines. Give me some ideas here, please.
Personally I treat in debt like the Poverty hindrance from Deadlands. The character, despite his best efforts, always winds up in Poverty with that flaw. A character with In Debt, that doesn't buy of the quality, quickly finds himself back in/still in debt. Either through an error, lender sleaze, or stupid bad luck. Maybe he dives for cover in that nice restaurant during a firefight and shatters a 30,000¥ glass sculpture, maybe that traffic cam caught a spoof chipped vehicle sliding into that Westwind that matches
his registered vehicle's legal registration, maybe an old Johnson has decided it's the perfect time to blackmail him, or maybe...just maybe...he's suddenly having to pay back child support.