I'm not sure if this has already been brought up and I'm not sure if this is the right place to be posting this, but I thought I'd try anyway.
I'm playing on PC (MS Store version) and I've noticed that after I've completed a companion's personal quest and gained their bonus perk, I'll lose the bonus perk after doing a respec. HOWEVER, after doing a respec, I'll get an additional perk point to use for any companion who's personal quest I've completed as if it's giving me an extra point for the bonus perk.
That doesn't seem like it's how it was intended to work. I figured the bonus perk would be a permanent passive quest reward. The way it's working now you have no warning that a respec will remove the perk and no way of getting it back even though you do get an additional point to spend after respec.
Sorry if this is a well known bug, I just noticed it happening. I did a quick Google search and only found one small topic on Reddit talking about it. Figured I'd bring it up. Maybe someone else could do some testing to see if they get the same results.