It turned out that my initial analysis of bug 2026 was wrong. Read http://bugzilla.lyx.org/show_bug.cgi?id=2026 for details.
The summary is that lyx2lyx has the layout name "Standard" hardcoded in several places, and that it will make documents of classes without the layout "Standard" invalid that contain things like ERT, comments, some kinds of boxes and some other things. José proposed the following solution: - use a new optional argument, as you can imagine related to the package "Standard Layout". The default argument of it being "Standard". This suggestion avoids complications, one of them being reading the corresponding textclass files. Replace then all references to Standard with file.default_layout (this being the new value read from the argument). Then in lyx it is enough to pass this argument to lyx2lyx. This seems a simple fix, and it works retroactively. I know that it is late, but since this is a serious problem IMHO, I ask nevertheless: Do we want that for 1.4.0/1.3.7? Georg