Sounds like you needed to use something like Slack for office communication. It's very important that everyone adjusts their habits to integrate remote working rather than just the ones who are remote. When the communication stays within 4 walls but some of the team is not within those walls then problems such as yours arise.
It's impossible to get people to really do this if you have 98 of them in an office and 2 of them remote. You can try to mandate it, but people are going to revert to human-talk. If you're serious about a mixed environment of remote and in-person workers, you must develop systems that account for the resolution the remote workers will inevitably lose.
Not really - everyone was always on IM and I'd be phoning up and talking with people daily. But really I needed physical presence to really pick up on the subvocal stuff, and the people who would pop by and mention things off hand.