SUSE Manager Server Check in

I was wondering if there was a command to force SUSE Manager to check in with without re-registering the system?

Not clear what you’re looking for.

Every time you navigate to Admin>Setup Wizard > Organization Credentials (/rhn/admin/setup/, SUSE Manager connects to SCC checking your subscriptions and available products.

SUSE Manager Server itself, being based on SLES 12 SP3, uses the normal SLES registration means (aka ‘SUSEConnect’) to register itself with SCC. See the SLES documentation for further details.