Yes, multi-layering is specially useful for that exact reasons
Alpha <whatever> is up! Click here(Here's the official-ish thread at Flixel Forums for more info)-- Maps are always compatible with newer application versions --NOTES:Each time you save a ".flan" file, if the file already exists it's renamed with a ".flan.bak" extension.
Anyway you should backup your files periodically in case of corruption.
SUGGESTION FOR PROTOTYPING:For prototyping, use one layer AND one tileset for non-collidable tiles and another pair for collidable tiles.
This way you won't have to replace a lot of tiles when adding more non-collidable tiles.
The non-collidables first collidable index could be set really high to forget about it.
ALPHA 5+ Export/Import de sprite type lists, in case you changed a map and want to carry that list to other similar ones
(Experimental, save your work before trying!)
+ Full layer tile replacement (all of indexA to indexB).
It's awful and tedious but, for now, it's quite functional (specially for the "expansion" of tilesets)
+ Added map name to the title of the application for knowing what you're working on.
+ You can now set the "Package" for the exported ".as" files, to match the path you want.
* Corrected generation of code for addition of sprites (_map.addSprites...)
* Sprite tool: If not aligned to grid, there is no tile selection square when adding sprites (that usually bothers)
* Warning message if you want to remove a layer (before it just dissapeared). I think it would be nice as this is not undoable.
* If not grid aligned, sprites are put centered to the cursor (instead of top-left aligned as before)
* Fixed weird-rect-for-text-labels bug (reverted to old revision of wxWidgets)
* Fixed: deletion of sprite type didn't remove sprites of that type.