So I am not sure if this has been asked before but I have searched every major forum, wiki, and random things I found on Google for an answer. What I have found either didn't help/work or didn't make a bit of sense to me.

The issue I am having is this: when I use a tile set swap program they swap just fine, but when I want to swap to a different one, the tiles I had in place from the other one change on the map. Now I know some of you will think this is a rather dumb question but I don't really care I just want a fix/answer to this. x_x

The first screenshot is what I want in place, the second is after I change to a different tile set. If there is a way to fix this, any way of doing so would be more than helpful. I don't care if it is an easy or difficult method, one that works will make me more than grateful.

Assuming you are talking about SwapXT, the swaps save in the SwapXT program, not the VX editor. In other words, every time you switch to a new tileset using SwapXT, all maps in your project will change; but as long as you've saved the swapped map ID's in SwapXT, you should see the correct tiles when playing the game. It's one of the least favorite features about SwapXT, because it means you don't have quick access to correcting or adding to your maps without first having to toggle the tilesets with SwapXT every time you want to look at a new map with a different tileset.