@neilferreri’s comment made me remember I once had a similar problem where for some reason my GRBL has lost its G28 reference, this may have happened to you if nothing else changed in your workflow.
Quick fix: home the machine, send “G28.1” (without the quotes) using the MDI.
If as I suspect you are using the Carbide3d post.processor in Fusion, you don’t have the option to disable G28 retracts (at least the version I have installed doesn’t). You can (and should) reset G28 using the G28.1 command as decribed above, you could also jump ship and install @neilferreri’s most excellent post processor for the Shapeoko, and then you’ll have the ability to customize whether you want G28 retracts or not (as well as other options)