As far as I know, authenticated users shouldn't disappear on a policy installation.
As an example, see: https://support.checkpoint.com/results/sk/sk79060
As such, I recommend a TAC case: https://help.checkpoint.com
On the more general subject of Linux users with Identity Awareness, they can be authenticated with Active Directory like Windows machines.
Which means you should be able to use Identity Collector or Kerberos to acquire the identities.
That assumes the Linux machines are tied into Active Directory, of curse.
To the best of my knowledge there are no plans to implement a native VPN client or Identity Awareness client for Linux.
Requests for these items should be discussed with your local Check Point office.