After learning the grimoire slam skill with Aloth, it now has become permanently disabled even though it shows as having a charge available whether its in or out of battle.

Had the same issue; after installing latest patchest for Linux as of today the issue persisted, so I fixed my savegame like this:

http://pastebin.com/m4gGePNm

 

You'll need a working Python interpreter (most Linux distros do) or do the fix youself using a hexeditor.

1) Unzip savegame

2) Make a copy

3) Run script

4) Zip the savegame and replace in the game

 

Remember about backups, and best - do it after resting so it won't reenable something it should - to keep the game fair.

# Fix Pillars of Eternity save game with locked 1 per Encounter ability (In my case Grimoire Slam)
 
# mkdir save
# cd save
# unzip ../*.savegame # unzip only one you want to fix
# cp MobileObjects.save  MobileObjects.save_ORIG
 
# Run in python interpreter:
 
import re
data = open('MobileObjects.save_ORIG').read()
 
# Fix / patch (selected as the most common in my savegame)
good='m_activated\x06\x01\x11\x01\x06\x01\x00\x06\x01'
 
# Pattern to find and fix (only 1 occurence in my savegame)
pattern='m_activated\x06\x01\x11\x01' + '\x06\x01\x01\x06\x01'
fixed = re.sub(pattern, good, data)
 
f = open('MobileObjects.save', 'w')
f.write(fixed)
f.close()
 
 
# zip -r 'savegamename.savegame' *
# cp savegamename.savegame ..
# Try loading