Try running this bash script, it will recompile all .scpt files inside ~/Library/Application\ Support/Alfred\ 2/Alfred.alfredpreferences/workflows
cd ~/Library/Application\ Support/Alfred\ 2/Alfred.alfredpreferences/workflows
for f in user.workflow.*/*.scpt; do
plaintext=$(osadecompile "$f")
# | sponge |
echo "$plaintext" | osacompile -o "$f"
echo "Recompiled $f"
done