Adding + X gp abilities, such as "Everbright" in Magic Item Compendium, to an existing Specific Weapons will not cause that much problem I guess.
But adding abilities with "+X bonus" base price modifier or increasing existing enhancement bonus may cause game-balance issues.
Basically, there is no clear rule written in DMG.
But IMHO, It is really a bad idea to consider specific weapon's unique abilities to be +X gp abilities. If you treat Sword of Subtlety as a +1 weapon with +X gp ability for the purpose of improving it, it well easily become a no-brainer cheese to increase it's enhancement bonus.
If I were a DM, I will basically treat all the abilities of a specific weapons to be counted as if "+X bonus" properties. Many of the specific weapons do not have cost matches to the value of +X weapons. In those cases, I will treat that as a next higher +X weapon.
I mean,
Specific weapon cost (minus the cost of a non-magic weapon)
up to 2,000gp .... +1
up to 8,000gp .... +2
up to 18,000gp .... +3
up to 32,000gp .... +4
up to 50,000gp .... +5
up to 72,000gp .... +6
up to 98,000gp .... +7
up to 128,000gp .... +8
up to 162,000gp .... +9
up to 200,000gp .... +10
and so on.
For example, Sword of Subtlety costs 22,310gp. So I consider it to be a +4 weapon when adding more abilities or raising it's enhancement bonus. So, if you tries to increase it's enhancement bonus by 1 (to +2), the cost will be 50,000 - 32,000 = 18,000gp.
I am not sure this is enough to prevent cheeses for all the specific weapons. But it could be a good start.