Not sure what TSBs you showed the dealer previously, but 07-40-009-1 and
07-40-010 have little new in them. They're basically old TSBs redone to utilize the newer diagnostic equipment. Their purpose is to equip the technician with the information to properly diagnose a harsh engagement or a harsh shift. The warrantability depends on the item causing the problem. Keep in mind that "normal operation" is one possible conclusion based on these TSBs.
The warranties will be as follows: Transmission: 10/100 (powertrain) PCM: 8/80 (federally mandated emissions) TCM: 5/60 (bumper-to-bumper) Normal: none (no defect).
If the shop goes through the procedure in the TSB, you should expect that the diagnosis will be covered if the faulty part is still covered. Otherwise, you should expect to pay for the diagnostic expense.
I'll say that none of these TSBs relate to anything having to do with a speed sensor. I'll also say that very rarely is the computer (PCM or TCM) the issue. In my experience, the most common finding is a defective transmission, followed distantly by normal operation. I don't recall ever seeing a defective computer actually cause a harsh engagement or shift, but do agree it's possible.
I find the statement "wasn't related and didn't need fixing or if it DID, it was related to the speed sensor" a little odd. Exactly how is the service manager able to associate a something that doesn't need fixing (normal condition) to what it is that might need to be fixed. Sounds like BS to me, too. If it's normal, say so. If it isn't say so.
If you're interested, I can tell you whether you have a PCM (powertrain control module) or separate TCM (transmission control module) if you let me know the year of your Sonata and which engine it has.
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