You can change that form so that each time a value from any pop-up is chosen everything else is saved. This can also be done on a refresh or outright submit - there's no reason to have to lose the contents already entered. That might mitigate the contents being lost. You can also use javascript to periodically save, but that's not something I've implemented myself, so I don't have any person feedback to give about it.

An easy way to do it is to post all the variables back to the page itself when the refresh or submit happens.

You can also use a session file to save everything and load it back when the form resets/submits. I do either of these in all my PHP forms to keep them self-contained (as opposed to some scripts passing off data to another script, etc.)

With regards to the timeout, I can't say for certain without seeing the code (don't know if anyone else can either). A plain HTML form doesn't have a time limit of any kind that I know of, so there's something else at play here. Do you have any database access? Third-party library access? There's probably some session/cookie data being used for security and that's likely now in conflict with the server settings at GoDaddy (Perl/Apache, etc.. config files)