A main quest is an event you were meant to have to do in order to beat the game. Using glitches, some of the main quests, you can do without first doing earlier main quests. One such event is beat a later dungeon than one you have not yet beaten. If you beat a dungeon with a fused shadow, the game assumes you already beat all the earlier dungeons with a fused shadow and if you beat a dungeon with a mirror shard, the game assumes you already beat all the earlier dungeons with mirror shards. It is not however the case that doing any main quest will make the game assume you did all earlier main quests. For example, getting the Early Master Sword probable doesn't change which of any of the other main quests the game assumes you did. The game was probably programmed in such a way that after you beat Lakebed Temple, you have to hurry to Zelda and after that, you can go straight to the desert as soon as you become a human so if you got the Master Sword early, you can go straight there. Also, beating the bokoblins in front of the Forest Temple and releasing the monkey before you get the wooden sword doesn't make the game assume you have the wooden sword. The game probably treats all areas covered in twilight seperately; when ever you clear one area of twilight, no other area gets cleared of twilight and there's no change in which dungeons the game assumes you beat.