I do however agree that Construct shouldn't save all that extra data to the project. I think that is an oversight, and at that point the data should be truncated, much like nobody expects undo to still be there after opening a project, in order to save memory.
Ashley This sounds like a reasonable solution, thanks.
My only concern is that some people may temporarily shrink tilemaps while working on them. For example, if a map consists of three layered tilemaps, they might shrink the top two while editing the bottom one. If the project is saved in that state, any data in the shrunken tilemaps would be permanently lost.