That is an interesting rule Robbie, haven't heard of that one before. Nice thing Draft Buddy is pretty flexible to handle weird rules
Here is what I'm thinking... add an extra round to your draft, so if it goes to 13 then make it 14 on the rules tab. You will have to Compile Cheatsheets again to update the draft report tab, but change reset keepers and reset draft picks to no first so you don't lose any players (keepers) or draft pick trades you already input.
Then go to the draft report tab down to round 6 and put "** Pick skipped **" for each pick where you think someone is going to keep a player. And of course you can add this later, or select and delete (or Edit > Clear Contents) to remove if things change on draft night.
Do the opposite in round 14. Input "** Pick skipped **" for teams that are not keeping a player.
I think that works, right? Teams will then not have a 6th round pick if they kept a player but will have a 14th round pick. Make sense?