No this method has been foolproof for me. When you do an iTunes backup restore literally every bit of detail about your jailbreak, all your tweak, preferences etc. are retained.

We’re not always on the same level of luck, resetting iphone or restoring while jailbroken could be a nightmare to some. 

Long shot? I've done it 5+ times, always fixed this tweak I have.

[Tip] [AtYourOwnRisk] If your phone starts playing up (tweaks stop working etc.) you can restore from backup from iTunes to get it working again