CSA,
I take it you mean the short track on the toerail starting aft of the cabin structure.
Is your plan to replace with straight track thru the deck? If so what is your reasoning, foot clearance with respect to the running line?
It should be a question of preference. Personally, I would leave the track as it also maintaines bolting of the hull flange to the topside mold.
My thought is why interfere with this presealed condition, In addition, the track may be useful for other purposes not thought of yet. I have a 1980 cat30 with tracks on the deck and it's an inconvenience for stepping around also.
So in ending, it will be your decision if relocating your tracks will be worth the hassel. Good luck in your choice.
CR