arm64: base-files: fix upgrade issue when partition sizes are different

The call to remove partitions from the kernel was happening after the
new image was dd'ed, causing the "new" partitions to have minor
numbers offset by the old ones (e.g 4,5 instead of 1,2)

This caused export_partdevice to fail in platform_copy_config
1 job for arm64_2102 in 61 minutes and 23 seconds (queued for 2 minutes and 16 seconds)
Status Name Job ID Coverage
passed build_disk #1901590925
dynamic dynamic_runner_x86_aws x86