Print the depreciation schedule to PDF before changing the method. Put the printout in your file, in case the assets are placed back into service.

In the depreciation screen, the grid at the top shows the form each asset is linked to and the method used. Setting the form to 4562 only doesn't suspend depreciation; it just keeps it from going anywhere else on the return. Setting the method to 99 suspends depreciation entirely. Doing both lets you delete the Schedule E and not get a grumpy diagnostic.