FlexNet has the management utility "lmutil" which can be used for forcing license check-in (lmremove).
The general command scheme is:
lmutil lmremove -c LicenseFile.lic <feature> <user> <host> <display>
or
lmutil lmremove -c LicenseFile.lic -h <feature> <LM_Server> <port> <handle>
I think you need the license file to make things work, so try it with and possibly also without the -c parameter. Should look something like this.
lmutil lmremove -c LicenseFile.lic ARC/INFO GEOGEO GEOGEOsMachine "#2L\w {O"
or like this
lmutil lmremove -h ARC/INFO licenseserver 27000 305
You get these infos by using lmutil's lmstat command
lmutil lmstat -a -c <port>@<host>
As this works slightly different with different versions of FlexLM, you have to try should take a look in lmutils command reference on your installation.
EDIT: FlexNET uses Port numbers 27000 to 27005 by default, you can find out which one is living, by calling "netstat -a" on the server machine.