why restore the transporter patterns to their components rather than their Tuvix’d counterparts?
Counterpoint: why would you restore the transporter merges? The Tuvix'd contingent occupies the exact same state as the original individuals: "dead", destroyed in the process of recreating another, larger being. Reverting to those obviously unstable and dangerous merged beings instead of the individuals who had been merged to create them would be absurd.
That happened at least once, when Quark's employees formed a union and went on strike. I believe Sisko went to that well a number of times when Quark crossed a line or refused to do something important.
Really, it makes sense. Quark is profiting hugely from the Federation's willingness to not only give him a bunch of business but also not collect on some key expenses. That's a great business arrangement, but also gives the Federation leverage over someone they wouldn't otherwise have any trust in.