Hmmm, I was contemplating that but it seems like with the areas using g/s tiles mostly it'd be easier just to stick with those. It is well within your power right now to do a pokemon3d:hd patch, if you were willing.
All retexturing that changes the texture resolution will require changes to maps, this is because tile sets are done as a texture atlas, its multiple tiles in a single image. this is woodtower, the tile set i made for sprout tower, its an old version though, nilllzz ended up using the map and changed some of it to make it look nicer
so lets look at the floor in sprout tower floor 1
Code:
Floor:
right:
{"Floor"{ENT[{"Size"{intArr[8,18]}}{"Position"{intArr[-1,0,-1]}}{"TexturePath"{str[WoodTower]}}{"Texture"{rec[0,0,16,16]}}]}}
left:
{"Floor"{ENT[{"Size"{intArr[8,18]}}{"Position"{intArr[9,0,-1]}}{"TexturePath"{str[WoodTower]}}{"Texture"{rec[0,0,16,16]}}]}}
middle:
{"Floor"{ENT[{"Size"{intArr[2,6]}}{"Position"{intArr[7,0,9]}}{"TexturePath"{str[WoodTower]}}{"Texture"{rec[0,0,16,16]}}]}}
{"Floor"{ENT[{"Size"{intArr[2,8]}}{"Position"{intArr[7,0,-1]}}{"TexturePath"{str[WoodTower]}}{"Texture"{rec[0,0,16,16]}}]}}
mat:
{"Floor"{ENT[{"Size"{intArr[1,1]}}{"Position"{intArr[7,0,15]}}{"TexturePath"{str[WoodTower]}}{"Texture"{rec[16,32,16,16]}}]}}
{"Floor"{ENT[{"Size"{intArr[1,1]}}{"Position"{intArr[8,0,15]}}{"TexturePath"{str[WoodTower]}}{"Texture"{rec[32,32,16,16]}}]}}
strip after mat:
{"Floor"{ENT[{"Size"{intArr[2,2]}}{"Position"{intArr[7,0,16]}}{"TexturePath"{str[WoodTower]}}{"Texture"{rec[0,0,16,16]}}]}}
The parts you need to edit are TexturePath and Texture. TexturePath is the name of the xnb from the textures folder you are using. if you have it in a new folder inside textures you need to specify folder, so say your stuff was in Textures/HD you would set it to
{"TexturePath"{str[HD\WoodTower]}}
but you could just name your tile sets like WoodTowerGen4 or HD or HGSS or w/e you wanted. I would advise against making your stuff actually overwrite the official maps. You can easily copy the maps and textures and edit those copies, there is room for both that way.
the other subtag is texture, it takes 4 arguments, the first 2 say where to start from in the image. For the floor texture that is 0,0, the top left corner of the set. the mat is made of 2 floor blocks with different textures applied, 16,32 and 32,32, check where they are in my set. basically, you need to tell it the pixel the top left corner of your tile is in the image.
The other 2 arguments are the tile size. this is how big your tile is, in pixels. all of mine are 16x16. if you are going to use hg/ss ones they will be much larger. this is why replacing the textures with bigger ones won't work straight away. You can just copy the map files and edit all the texturepaths and texture subtags to suit, you wouldn't have to remake the map itself. certain things changed about layout in hg/ss that'd need some mapping to do, but for the most part you can use copies of the official maps to do it.