old iphone, new itunes? what to do?

[piedrafina]

i just jailbroke a phone for the second time in my life last night and i have a few questions, but rather than put them all in a lengthy post, i'm posting them seprarately since they are unrelated (i think).

my partner had my partner has had a jailbroken, unlocked iphone 3gs with ios 3.1.3 and firmware 5.12.1 installed, she switched to a spare iphone we had because it was acting buggy. the spare is a 3gs, same ios. so, i have now updated to 4.2.1 (restored in itunes) and re-jailbroken it with the baseband update. in the time since the first jailbreak and now, she has gotten a new computer with itunes 10.1 on it. to avoid problems, she has been syncing her iphone with her laptop, which had an older version of itunes.

so, having given you all the whole background story, my question is this:

how should she go about syncing now? the contacts are in both places, so that is not the problem. what we want to get back are the apps. she has the old phone with all her apps on it, and the freshly jailbroken one with no apps. all the apps she has downloaded have been from the app store. none at all were jailbroken apps, so there is no cydia blob (can't remember what those things are called). she authorized her new computer for her itunes account, but the only apps that show up in the library are the ipod touch apps she has downloaded there (which are on a different itunes account). if she syncs the old iphone to the new itunes, what will happen? can she sync the freshly jailbroken one with the older version of itunes?

[iYeow]

If the old itunes and new itunes is signed in and authorised under her name, when she start sycing with new itunes, itunes will ask if you want your apps from this old iphone to be transferred back to itunes.
If the freshly jailbroken iphone with old itunes, she has to check mark the app in itunes to be able to synce onto the freshly jailbroken iphone.
If her new computer has no contacts yet, when you sync with an iphone that has contacts, make sure you choose merge when itunes asked you, otherwise your iphone will lose all the contacts.

[piedrafina]

when we originally jailbroke her old iphone, the instructions we were given said we could not upgrade itunes or we would mess up the jailbreak. we haven't bothered to read up on jailbreaking at all since then, so i'm not sure if that is true or not.

so far we have transferred the apps from the old phone to the computer with itunes 10.1 but haven't synced yet.