my tileset is a mess, i have blocks that should be togheter but are not.
If I move them I mess the entire level, so is there a solution to regorup my tiles and move them in the tileset image without messing the entire level or reindexing it?
Or again do a 1:1 tiles swap on all tmx/map/layers?
Unfortunately this is still an unsolved issue. Proposed solutions could include some tool to change the tileset with, which would be able to fix up maps at the same time, or to reference tiles indirectly so that their visual area can be changed without affecting their tile ID.
This is a feature I could provide in the short-term, so that fixing up a map when some tiles have been moved may be easier. There is a pull request open for this which I intended to merge since a while already.