How to get PTC to use new license instead of old one?

When licenses expire (assuming you are working with subscription licenses) you need to replace the outdated license file on the license server with a new one you get from PTC. The instructions I wrote up for our folks to do this are as follows:

The Creo license file must be updated on a yearly basis. Doing so is somewhat simple, but
can have troublesome ramifications if not done properly. Here's how it's done:

(1) Obtain the new license file from PTC. If no changes have been made to the configuration
 of the server (new name, Host ID, etc.), this can be done with a simple web inquiry.
(2) Copy that file to the desktop of the server. You're going to be modifying it based upon
 the settings of the currently active license file.
(3) Traverse the directory tree to the current license file. It will be in a directory that
 is of the format:

 C:\Program Files\PTC\FLEXnet Admin License Server\licensing\license.dat

(4) Open the current license file, and verify that the PTC Host ID and other info in the
 comments (lines that begin with "#") agree with the new license file. If all is okay,
 copy the two lines that start with "SERVER" and "DAEMON". These lines should look
 something like:

 SERVER INNOVENT-LIC PTC_HOSTID=XX-XX-XX-XX-XX-XX 7788

 DAEMON ptc_d "C:\Program Files\PTC\FLEXnet Admin License Server\x86e_win64\obj\ptc_d.exe" "C:\Program Files\PTC\FLEXnet Admin License Server\licensing\ptc.opt" 

 These two lines tell the licensing software what computer is being used to host the
 license, and the paths to the software it needs to run. 
(5) Open the new license file on the desktop, and replace the two "SERVER" and "DAEMON"
 lines with the ones copied from the current license file.
(6) Run the "Services" program to bring up the list of all running software services.
(7) Scroll down to the "lmadmin_ptc" service.
(8) Using the right mouse button, STOP that service.
(9) Rename the current license file in the Program Files\PTC\FLEX... directory to
 "license-old.dat". This is done as a precaution in case something was not done
 correctly, so things can be reverted back to the previous state.
(10) Rename the new license file on the desktop to "license.dat".
(11) Move/copy the new "license.dat" file to the Program Files\PTC\FLEX... directory.
(12) In the Services program, right click on the "lmadmin_ptc" entry and hit "Start".
(13) The lmadmin_ptc program should now have a status of "Running".
(14) Verify that things are okay by running "ptcstatus" on one of the computers in the
 network, or by trying to run Creo.
(15) If all is well, you are done. Close all the programs and files involved, and log
 out of the server.

Hopefully this makes sense to you. The big roadblocks in fixing these things are having the right permissions to change things on the server and getting the new license file from PTC.

Did you restart the license server to activate the license file after you installed it?

Putting the file in the license location is only 1 step in the process.

You need to have the license management software read the file and then restart the license manager.