does Hydrochloric Acid react with PET?
You can etch ITO on PTE by mean of conc. HCl solution without problems. The treatment duration depends on the ITO thickness but is limited to minutes.

Just make few samples (residuals from cutting etc will suffice to make this test) to find out how long it takes to fully remove ITO.

No reference need it as I do etching of ITO coated PTE electrodes since years.

For sake of completeness let me add that I never investigated PTE itself prior and after the etching so I do not know if there are changes which, for instance, may interfere with long (very long) stability etc.

In my case it suffices that PTE maintains its transparency and still behave as a robust but flexible substrate. It seems it could be your case, too.

Just to be pedantic. Obviously after etching the foil must be washed thoroughly.