Just don't connect the skills to attributes. Delete everything linkage related in the skills component. Or, if there's a default ability for each, present that, but make it clear whether you're presenting Investigation or Investigation+Perception (assuming perception is the default). Since both the skill and attribute will be listed on the summary panels, or on the character sheet, they'll both be displayed near each other, so the user can add them himself. If the game system doesn't make a linkage between two things, you shouldn't do so in HL, either.
Alternative 2: If the game system links each skill to a limited set (if it's ever more than 3 go with the first alternative) - so, if every skill, like your example, lists no more than three alternatives, you can take a look at how the first linkage on the skill component is defined, and how it's used, then duplicate that, creating linkages attribute2 and attribute3 (and make these linkages optional). Then, you duplicate the SklRoll field to get SklRoll2 and SklRoll3, and modify the script to use a different linkage (and remember to account for there possibly not being a linkage, since you made it optional). When you display the skill, you can display the skill's base value, and/or one or more of the SklRoll displays, depending on the space you have available and what the user will want to know, at a glance, when they're looking at that page.
Disign philosophy comment - the Skeleton files are an attempt to supply the user with common behaviors that exist in many RPGs. Just because the Skeleton files does it some way doesn't mean you have to do it that way if the game system you're working on doesn't do it that way.