Q: My sister and I have shared an iTunes Store account up until now, but due to iCloud we would like to switch and use different accounts. If I make a new account, will all my purchases made by the old one disappear from my iTunes?
A: For locally stored content, the answer is basically no. Anything already in your iTunes library or on any of your iOS devices will continue to be available regardless of which iTunes Store account you are signed in with.
Essentially, the account specified in the iTunes & App Stores settings on iOS is simply the default account for new purchases and does not affect access to any existing content already loaded onto your device, whether that be music, videos or even apps.
The same is true of iTunes on your Mac or PC.
As long as your computer remains authorized for the other iTunes Store accounts, it does not matter which account you are currently signed in with; content already in your library will remain in place and you can still access it and sync it directly from there to any iOS device connected to your library. Switching to a different iTunes Store account will not de-authorize your existing computer, but should you ever want to move your iTunes library to a new computer you will need to ensure that it is authorized for the original iTunes Store account in order to access your previously purchased items.
The notable exception to this is for Apple’s iTunes in the Cloud and iTunes Match features. If you are using iTunes Match, then switching to a different account will essentially remove your iTunes Match library. For iTunes, this means any music that is not stored locally.
For an iOS device this basically means your entire music library, since iTunes Match, when enabled, effectively becomes your library on an iOS device. In this case you would either need to subscribe to iTunes Match under the new account, or simply go back to synchronizing your music directly from iTunes over USB or Wi-Fi.
The ability to re-download previous purchases will also be affected by switching to a new iTunes Store account. In order to discourage people from simply hopping onto their friends’ iTunes Store accounts to download content, Apple has enforced a 90-day restriction on downloading content with a new account. In other words, after the first time you switch to a new iTunes Store account, you will not be able to switch back and re-download any purchased items directly from the iTunes Store for 90 days.