Have you tried bonding it to different Eras to see whether you may have a suspect Era? A diagnostics report and a call to Sonos support may also be worthwhile. 

I was thinking of pairing it to another Era 300, but after I connected the Sub to the rear right Era 300 it asked to complete Trueplay again this time both the sub and speaker calibrated it seems.

Maybe I connect it without doing Trueplay? 

For peace of mind I’d connect it again to the original one and see (hear) what happens. If it’s still not right you may have a faulty Era. 

So I connected to another Era 300, then back to the original, then even an Era 100, output on the Sub was identical, non-existent. While I was connected to the Era 100 I adjusted the bass on the EQ and the Sub was hitting harder and I could turn down the bass volume, but when all EQs and gains are flat the sub virtually has no output. 

When connected to the Play 3s, tuning the sub gain to 3 it was very deep for base, i could not take it much higher before.