I can only speak after years in the action figure game (got out a several years ago, thank God) but I believe they would be similar in multiple respects.
If someone is looking for a rare collectible whatever, they will always pay more for original packaging, documentation, etc. Conversely, they will tend to want to pay less if those materials aren't present. Thinking about aftermarket modification, I turn to my years in the car modification hobby. I've seen a LOT of guys try to sell their modified hot rods for big money, only to be disappointed when they don't sell. At that point, they're forced to remove their modifications to sell the car nearer black book, and then try to sell the parts on the Bay separately. Now, I DO think that there are more knife guys who'll take a modified knife, since there's less of a chance of having an item whose modifications have caused a bunch of new issues.
But that said, I'm not sure how you'd valuate a modified knife. If it's as simple as a lanyard or aftermarket clip, you can always try to ask for the cost of the bead or whatever. Worst that can happen is someone PMs you with an offer less than what you're asking for.