We have a large number of Office 365 (Not for Profit) Enterprise E2 licenses (which I'm sure we bought as E1s).
We've recently attempted to try audio conferencing, and so have bought Audio Conferencing (Nonprofit) licenses. However, we get an error stating that Audio Conferencing cant be used without Enterprise E1 licenses. Does this mean we have to replace all our E2 with E1? I thought they were the same.
Yes, that sounds like what you will need to do, though I'd speak with a Microsoft licencing rep or partner to get precise advice. E2 was discontinued years ago, 2013 by some accounts, though there is little information about it.
Ah, that's interesting, perhaps talk with support and get them to correct the offering, if they can do that as it's preventing your use of Office 365. Sounds like an anomaly or something didn't happen when it was supposed to.