I use the Warp tool (“Tools/Transform tools/Warp transform”) fairly often. It’s very easy to make a lot of changes on a layer and then for example switch to a new layer, at which point all the changes are lost.
If something like this is what’s happening in your case, the solution is to make your changes on a given layer, then hit the Enter key before you do anything else. This “commits” the changes you just made. Otherwise, sometimes (but not always, depending on exactly what the next thing you do actually is) those changes are lost.
There’s an open bug report on this issue:
If none of this sounds like what’s happening in your case, then the next questions would be what operating system, what version of GIMP, what exact steps, etc.