Seems windows' urge to suggest formatting the linux partition can be an issue with using the same sd card for both stand alone and raspberry pi operation.
Might have a play with different partition types to see if that is avoidable or if its feasible to just remove the second parition from the partition table and recreate it on first boot if needed. (obviously it'd be better to tell windows to fยค"!% off and leave well enough alone, but..)
edit:
Changing the partition type to 0 (empty) seems to prevent windows from trying to display, mount and format the partition while allowing grub to boot linux based of the UUID of the ext4 partition as well as retain the device node.
label: dos
label-id: 0xfb28cfac
device: /dev/mmcblk0
unit: sectors
/dev/mmcblk0p1 : start= 8192, size= 524289, type=c
/dev/mmcblk0p2 : start= 540672, size= 30575616, type=0