It's fine. Removing app never happen automatically. The thing you able to install on iPhone is copies/transferred in iTunes. That's all. Even if you are using cracked ipa's means you have "App sync" installed through cydia.
But if you sync with other iTunes and want to add music then it will erase all data from iPhone to create new iTunes files. In that case you must have backup of your previous iTunes backup. Like app music and all that. But this happens only if ou change your pc/ Mac.