every 2-4 hrs i have to recover 5 mossms, always different ones that haven't communicated. Anyone else having this issue?

Stephe are they close enough to their environments? 10 meters is the maximum space between environments or they can't see/sense them and stand still holding their tails, they don't talk to the mothership when that happens, if you don't have enough for them to do you can also get the same message, make sure they are close enough to the environments to find them. Another reason they give that message is when they are on merchant blocks.
You don't need to do recoveries every time they stop talking to the mothership. I was told by the Mossms team not worry about doing recoveries if you can see them out but getting that message, just pick them up and drop them back down or drag them in "edit" closer to where they have something to do and if on merchant blocks just ignore the message altogether.

Maybe totally wrong thinking, but I have the same when environments are too close to landborders

Altered is correct...
If a Mossm is not communicating it does not necessarily mean it is lost. Mossms only communicate with the Mothership if they are in an environment. If they are not in cryo and are doing anything else (auction block, live selling, standing still somewhere, in inventory) they will not be communicating. If they are not communicating and they are in environments and you can see them, just wait a while. They'll check in again and the message will go away.

We do realize some ability for sorting would be better so you can tell it which ones don't need to be communicating with the mothership right now. We'll enhance it when we can.