Yes, you can only run one version of flexlm. But make sure you run the latest version that you have installed.
First, look at your license.dat files, make sure the server lines are the same, and the hostid's match up.
Then combine the feature lines from both into one common file.
kill the lmgrd daemon(s) and then restart the daemons with something similar to:
/path-to-flex/lmgrd -c /path-to-license-file/license.dat -l /path-to-log-file/flexlog.log
Now - it is possible to run morethan one instance of flexlm, but if you have common feature lines in the two license files, you will run into trouble. One other issue is that you must make sure that your software supports the version of flex that you end up running, and as a result you may need new keys, if you are updating from flex4.x to flex 6.x for example.
good luck