The sync process will not alter or remove your App Store apps, nor your Cydia apps.
In some cases, however, tweaks from Cydia may cause apps to appear improperly on i Tunes.
For example, now i OS 10 is available to download now, after updating to i OS 10, you may lose your important apps on your i Phone during jailbreaking.
So, before creating a backup in advance seems quite necessary.
Can't Miss: How to Backup i Phone to Mac Note: For those jailbroken apps you download from Cydia, you can not backup with i Tunes or Any Trans yet.For example, if you hide apps on your phone using a jailbreak tweak, they will still appear on i Tunes on your computer.Despite the inconsistency, syncing will work correctly.Jailbreaking an i Phone, despite voiding your warranty, will not prevent you from continuing to use all the apps you've bought through the i Tunes App Store.Rather, the process adds an alternative app store, Cydia, to your phone, which works alongside the official App Store.You can download apps and system tweaks from Cydia while continuing to shop for apps from the i Tunes App Store.