Oh that is so sad. But it doesn't sound unsalvageable. It sounds like during those 3 years apart, something got a little lost and you're getting to know each other again in a day-to-day setting, which can be tiring, hard, mundane, especially when raising kids (sorry kids! We love you but...). Also, you probably had your own 'system' while coping and that's been disrupted by his return. You probably feel a bit of guilt too because you're supposed to be overjoyed that he's back in the family home, full-time. Well, it's a huge adjustment. Go easy on yourself, OP. It's going to be a bit wobbly.
He too would have had ways of going about his day-to-day life when the pair of you were apart.
It really sounds like you've just got to tighten up the loose connections- easier said than done, I know.
How are you finding being home with him day in and day out? How is he adapting to life as it is now?
I had a similar marriage in this respect: My MIL was as toxic as they come but lived in another country which helped. FIL was local to us, in our lives, an amazing soul and a real second father to me. His death was, like almost every loss, enormous. It opened up lots of old wounds and trauma for my then-husband. Toxic MIL had been on NC status, then became VLC following FIL's death, then regular weekly Skypes became a thing, etc. and it was so invasive and so damaging to my then-husband, to our marriage really (which was going to fail anyway and not because of anything to do with me or even his own family in the end). I really understand the low-level threat that comes with having a toxic MIL, even one who is VLC. I wonder if having him home full-time brings your toxic MIL that little, teeny, tiny bit more into the family picture. That in itself is another discomfort to come to terms with.
Anyway, reconnecting... it's something to talk about together- getting to know each other again as a couple, as a family. How are the kids doing with dad home all the time?
Take it easy. Cut each other slack, hug each other, understand that you are facing this difficult task of reconnecting but do so with love and patience (and with some good days out as a family, as a couple, you can do this). I hope you can find peace again in your marriage.
There really is always the possibility that maybe you've outgrown him. Maybe his presence in the home isn't a positive one for you and he's picking up on that. Just a thought. But sometimes, time calls time on a marriage and it's very sad but something that can't be reversed. I hope that's not the case, but it's ok to explore that possibility too. 