[chefandy]

For decades, Adobe has presented a clear text message in the save dialog box and appends a removable _copy to the file name if the format lacks layers/transparency/alpha/animation/CMYK support/the appropriate bit depth, etc. but it doesn't impede professional users' progress when they know what they're doing. It also doesn't change the representation of the document in memory so you can just save a fully-layered version right afterwards unless you manually reload the file from disk.

That approach warns less knowledgeable or hurried users when it looks like they're aiming the gun at their foot, but it still lets expert users follow through unimpeded. Figuring out how to communicate the risk to the user while not removing functionality is proper interface design. Simply not letting people do it is "dumbing it down," and one of many examples of why Gimp is not an appropriate choice for high-volume professional users despite its on-paper feature list.