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Hi quick question: if a dwarf puts weapon runes on a great weapon, does it still retain its strength and ap bonus?

Yes, it's still a Great Weapon. You'll note that some runes can only be applied to Hand Weapons, and also the section on Weapon Runes begins by saying that they can be engraved on hand or great weapons.

If the great weapon lost it's rules, then what would be the point?

Thank you. Was just checking as in the previous rules from Warhammer fantasy battles it lost its extra strength.

It used to lose the GW special rules because +2S on top of 3 mix-and-match magical effects was considered a bit OP.
Taking a GW used to be mostly for fluff purposes or in case of the rare magic-item-suppression effect.
Or for cheap Str bonus on a character without weapon runes decked out with all the defensive gear you could muster.