I just wanted to share my final script which works just fine.
Since the installed add-ons are not compatible for both linux and windows at a time, using same profile folder with -ProfileManager was a bit of useless thus I really needed this thing:
#!/bin/sh
DATE=`date +%F-%H%M%S`
HDA1="/mnt/hda1/Documents and Settings/username/Application Data/Mozilla/Firefox/Profiles/profile0.default"
HDA6=/home/user/.mozilla/firefox/profile1.default
mv -v $HDA6/bookmarks.html $HDA6/bookmarkbackups/bookmarks-$DATE.html
cp -v "$HDA1"/bookmarks.html "$HDA1"/bookmarkbackups/bookmarks$DATE.html
mv -v "$HDA1"/bookmarks.html $HDA6/bookmarks.html
firefox
cp -v $HDA6/bookmarks.html "$HDA1"/bookmarks.html
I hope it is useful for somebody else out there too
