That actually clarifies the original requested ruling here though - BV goes into discard, then lab goes into discard, then it can be pulled off by royal seal, but now because it stopped being the top of the discard pile for a second, even though it is now again, BV can't be pointed to as being 'when gained' by RS anymore, and so that effect fizzles.
Which would imply that... I'm still not sure on the top-deck-BV THEN gain another card thing. I am guessing you can't, but it doesn't seem entirely clear.
"Lose track" *only* stops cards from being moved. Once Border Village triggers, it will happen, there is just ordering to deal with. Border Village can end up trashed or whatever and that doesn't matter.
Just to make this more explicit for FAQ-readers coming to this thread:
1. You buy a Border Village; Royal Seal is in play. You intend to use BV's ability on a Lab, and you intend to top-deck as much as you can.
2. Assuming that no "When Buy" effects are relevant, the first thing that happens is the Gain -- you get BV on top of your discard.
3. Two things happen: (BV) "Gain a Lab"; (RS) "Put BV on top of deck". You can choose which happens first.
4. You decide to do (RS) first. Royal Seal looks for the BV on top of your discard pile; it's still there and hasn't been covered up. (RS) succeeds and the BV moves to the top of your deck.
5. Then (BV) happens. You gain a Lab, it goes on top of your discard.
6. Royal Seal now triggers on the Lab gain, and so the Lab moves from your discard to the top of your deck.
7. Net result: The top card of your deck is a Lab. The card underneath it is a Border Village.
Say you did the other choice in step 3. Then we get:
1. You buy a Border Village; Royal Seal is in play. You intend to use BV's ability on a Lab, and you intend to top-deck as much as you can.
2. Assuming that no "When Buy" effects are relevant, the first thing that happens is the Gain -- you get BV on top of your discard.
3. Two things happen: (BV) "Gain a Lab"; (RS) "Put BV on top of deck". You can choose which happens first.
4. You decide to do (BV) first. You gain a Lab, it goes on top of your discard. This covers up the Border Village, making everything (except for BV) lose track of it.
5. Royal Seal triggers on the Lab gain, and so the Lab moves from your discard to the top of your deck.
6. Now the (RS) thing from step 3 happens. Royal Seal looks for the BV on top of your discard pile; but since it was covered up, Royal Seal can't find the BV even though now it is back on top of your discard pile. (RS) fails and nothing is moved.
7. Net result: The top card of your deck is a Lab. The top card of your discard is a Border Village.