I've used patch 1.10 compatible version of debug console (not yet released, can be found in nexus mod comments), to spawn pristine crystal in the inventory, but it does not help since it does not advance the quest, so crystal can not be used to fix the portal.
EDIT:
I've used wrong crystal from Phillipa quest ('sq302_crystal').
This is the debug console command that should be used:
additem('th1009_crystal')
.
.
.
So, how to fix the issue, step by step:
1) Install debug console enabler from nexus:
http://www.nexusmods.com/witcher3/mods/143/?
2) check mod comments for updated
debug-console-enabler.dll that is compatible with patch 1.10
3) replace installed
debug-console-enabler.dll from official version of mod with version from step 2
4) start game and load the save
5) Open debug console with '~' or 'F2'
6) Type following command:
additem('th1009_crystal')
And that's it. It should advance the quest as if you picked up the crystal.