Overall AP License Limit - AP/PEF Licenses
On the controllers, APs terminated on the same controller, there is no control (in AOS 6.x) in how individual licenses are consumed. So if you have 100 AP licenses and only 50 PEF licenses, the controller will only enable 50 APs worth of connectivity. It is a software limitation unfortunately. AOS 8 has a tad more flexibility if you can split up the controllers that are terminating the APs that need PEF versus the ones that don't, but they still have to be on separate controllers.
If you don't need PEF and want all of your AP capacity, you would need to delete/remove your existing/current PEF/RFP/WebCC licenses so that all that is left is the AP license, then the controller will enable the rest of the APs.
Note: If/when you delete the PEF license, any custom roles used by any group will be removed. So if you have RAPs using PEF in the RAP or user roles and delete PEF, you will need to change the role to one of the default/canned roles on the controller without PEF.
You would be FAR better served to purchase the remaining PEF licenses you need, as PEF is a critical feature and functionality.