Ugh, sounds awful! However, you were able to apply to restore his status when the app was returned even though his IEC had expired? That's actually good news from my side of things. I've been stressed every day that if the app is returned for whatever reason, I will have to apply for a visitor visa. Or is that the status that he got as well?Ugh your story sounds familiar. I'm Canadian and my common-law partner is American, he was here on an IEC OWP and we left submitting the PR and OWP apps pretty late (although I was finishing my PhD so kinda legit reason). He was on implied status for almost 3 months before it was returned to me incomplete (2 days before I defended actually..), because I submitted my T1 General instead of my Notice of Assessment. Cost us $200 to apply to restore his status and of course IRCC had "updated" their forms since I originally submitted so I had to redo everything. Not to scare you, hopefully yours will be fine, but super disruptive with him having to quit working and me having to support us on my then not so great student salary..
I feel awful, poor guy hasn't been able to go home since Christmas and may not get to until the end of summer depending on how much they ding us for him being out of status. I wish you and your partner much better luck than us!!
I hope processing goes super fast for you! And congrats on the PhD!