Here's a nasty bug in the Qt version of LyX 1.3.2. I guess that it is present also in current cvs.
Open a file $HOME/Draft/mydoc.lyx Move the directory mv $HOME/Draft $HOME/docs/Draft Try and "Save As" the file. I can break out of the cycle of Error dialogs: ERROR Could not read the directory $HOME/Draft only by recreating the directory. This seems counter-intuitive given that I'm trying to rename the doc ;-) -- Angus