Settings can't be saved when using System->Settings->SaveSettings. It fails with message "Error saving settings! No flash space available".
Flash space for settings is scarce (64KB) and is used both by Alt-F and the vendor's firmware, so it is possible that no available flash space will exist when trying to save Alt-F settings, depending on the vendor's firmware settings.
Alt-F doesn't automatically remove the vendor's configuration files from flash in the eventuality that the user wants to reflash it back or Alt-F is being used through the reloaded (funplug) method. The only exception is that an unneeded file, named "system.log", is removed from flash. This will mitigate the problem, but will not solve it.
When Alt-F is flashed this problem does not happens, so settings can be safely cleared and it is possible to store several sets of settings, each one tagged with date/time of creation.
As there are two places in flash where to store settings, and Alt-F only uses one of them, the other always has the last vendor's settings; when re-flashing a vendor's firmware, Alt-F prompts you for recovering the vendor's settings stored in the second location into the first. It was not exhaustively tested if this will in fact fully restore the vendor's settings.
You are advised to upload and save the vendor's settings to your computer, using the vendor's firmware. You can do the same with Alt-F settings (from 0.1B7 onwards), but Alt-F will not save/upload the vendor's settings.
There is nothing more that can be done, this problem will be present for all future Alt-F releases when it is used using the reload method.
See also issue 13 for more details.