Sigil allows you to apply and remove both the Adobe and the IDPF font obfuscation schemes. I don't know exactly what ID does differently (I'm certainly assuming they use Adobe's scheme somehow), but perhaps you could use Sigil to remove the existing obfuscation; save and close ... and then reopen and reapply the Adobe font obfuscation, and save.
You have to right-click on each individual font-file in Sigil's book browser to check/uncheck the obfuscation.
That's all just a WAG from guy away from his computer, though. It may accomplish nothing.
I don't have InDesign, but if you could provide a tiny, non-copyright-infringing sample epub with an ID-embedded font, I'd be happy to take a look. Feel free to PM me if you've concerns about such a sample being available on a public forum.