Don't panic mate, you aren't in a unique position, most of us are in the same boat. I have similar mods and a mail-in ECU tune from USA.
When the TPS is back in stock you get the job done at Yamaha and that will wipe your flash. The bike will be perfectly rideable with your mods and the stock tune although you will have to re-fit the O2 sensor (i think). Then go to your tuner and get the reflash, after that remove your O2 sensor again. Job done.
I have to do the exact same process except I will need to post my ECU to America at the end. I've fitted a new TPS over winter and the bike hasn't turned a wheel since so I'm hoping my Yamaha dealer will just give me the ECU update and keep their fingers off everything else.