Yes, a reset of the primary TPS and long battery disconnect could have affected your PC3, although mine runs fine if only 1% off idle zero.
I assume you have the PC3 software on your computer to communicate with the PC3? Also, did you save a copy of your custom PC3 map on your computer? If yes, connect computer to PC3 and verify that your custom map is even still in PC3, and TPS readout of PC3. You can zero the PC3 TPS setting from menu, and reload your custom fuel map with the PC3 software. Also make sure nobody effed with the enrichening buttons on side of PC3 (should be zero with custom map). If it was me, I'd also double check Triumph dealer's setting of new TPS with Tuneboy (I don't trust most Triumph dealers to get it right).
If you don't have the PC3 software, you can get free copy from DynoJet website. The latest edition has acceleration pump controls for your PC3USB (good stuff). If you don't have a copy of your custom PC3 fuel map, maybe your dyno tuner can email a copy to you from his dyno computer. They usually save all custom maps.