I shared this issue back then in November 2021 so I'm going to copy-paste some of what I wrote in your Discord server. 
This is really my only problem right now with the mod, because other than that it is glorious.

Even though my config changes apparently do take effect immediately after /es_reload according to the altar UI, the moment I make actual use of the ability it still has the default cooldown.

Altar preview:

Lvl 50 Teleport still using the default 80s cd. This is in my server:

Single player worlds do not experience this. The new reduced cooldowns do work unlike the server.

Another ability which should have a 40s cd but instead kept using the default 25s:

Same files for both server and clients, issue persists no matter what (server reboot, new world, fresh new config files)

Same thing for the Heart Boost passive. However, tweaking the damage passive did seem to work after /es_reload
I did not try everything so there could be more.

To get around some of this I had to set a maximum level of 20 for every passive, as I am trying to release a modpack with this mod and balance is crucial.

Using the latest release:
EnderSkills-1.12.2-1.14.0.3

Forge 2860

Thank you for your time.

Yeah. I believe I have fixed it.