Hi Apple Loops are in your Loops Browser in Logic. That's why it's important to set a name and tags for them in the Apple Loops Utility or under Region > Add to Apple Loops.
If you set them as 'looping' and with an appropriate key you can use the Transposition global track to transpose all MIDI and apple loop regions in your project at different points of the project.
Here is an example of how to work with Global Tracks:
Alternatively, you can adjust the particular region's Transposition value by selecting it in the Arrange area and in the Inspector click-drag the Transposition value.
ALternatively, use the Pitch Shifter II plugin on the track and set the values as desired. You can automate these values over time... this will work on ay material on any type of track.
Let me know how you get on.