itunes backup after Absinthe 2.0.4 Jailbreak for Iphone 4S IOS 5.1.1 Question

[iphonefr33k]

I see, so what order would I do this? Let say I want to unjailbreak it. In the meantime I have a restore point that I would like to restore to.

1) Unjailbreak
2) Restore which was a backup of everything after the jailbreak
3) I made a PKGBackup backup so after the itunes restore then restore with PKGBackup?

ZIg9449 not sure how I would handle that if I cannot trust my jailbroke backup? WHat would the purpose be of doing any itunes backup after the jailbreak then? Maybe I misunderstood your point. DOes it have something to do with getting the free and paid apps from both the apple store and cydia mix that were backup'd that could cause some issue down the line maybe?

EDITED:

I bought the iphone 4s just a couple of weeks ago iOS v5.1.1. Maybe added two free apps and that was it. I then jailbroke it with absinthe 2.0.4. SInce then I have been installing several tweaks and apps and duing daily backups with PKGBackup and Itunes.

I will not be able to get back to the same point I was on my very last backup? The system will run unstable if i restore a itunes jailbroke backup?

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[bab2010]

Do you wish your iTunes backup files to hold cydia informations? if yes then you make a backup in iTunes after you have jailbreaked and install all tweaks/apps you want from cydia. Let's say that iTunes backup file is called "iTunesCydia backup file"
You factory restore the iOS to unjailbreak it, then restore back your "iTunesCydia backup file"
Use PKGBackup to restore your Cydia apps/tweaks.
After PKGBackup finish downloading and installing everything and respiring, you will notice that your cydia apps/tweaks settings are back to the way you set them up prior the "iTnuesCydia backup" and the factory reset.
Now having such an "iTunesCydia backup file" only can become annoying when there is file error or corrupted files within the system by the time you were performing the iTunes "iTunesCydia backup" In such a case where you do no have a proper iTunes backup file (one you made when your device wasn't jailbreaked yet) you will be forced to start everything from scratch.

[iphonefr33k]

I see what you mean now. Well since I am doing itune backups every other day that coincide with PKGBackup's I should have a copy that works before the corruption I suppose.

It comes down to the point where if I have to just do a ISPW restore for example them install the jailbreak, then as long as I have a list of free and paid apps I should be able to get them back worse case scenario since they are paid for and install them all back manually.

Just a pain in the arse to do this all manually if there is some corruption along the trail of those file backups.

I could also copy the Unix tree or the /private/var /Library and /System folders as well. I was successful in doing so with Iexplorer. On the other hand i-funbox bombs out on large transfers I think associated with the file executables attributes or some other cause I cannot pinpoint. Iexplorer makes a clone almost like cp -rf or resync commands.

Thanks for the help!!