Windows is never going to like an NTFS that has been touched by another OS even if it windows was completely shutdown during that time. Reading the NTFS partition might be okay. But, last I checked none of the Linux drivers could write without windows noticing and fouling things up. If that has changed it would be welcome news to me despite my warning use of windows.
If windows (and to a lesser extent that other OS) came bundled with some ability to mount, read, and write filesystems popular with other operating systems this wouldn’t be such a problem. One shouldn’t have to involve the network stack or 3rd party drivers just to share a partition on the same hardware or a portable drive with a modern file system.