Until ntfsfix is included again with LE using a Windoze box to clear the 'dirty' bit on the NTFS partitions is your only option, I'm afraid.
The ntfsfix utility has never been shipped with LE, and I've closed the pull-request that proposed adding it because it's an incomplete tool. From a support and data integrity perspective it's better to inconvenience users by forcing them to use the right tool (chkdsk.exe on Windows) than not-quite fixing the problems a filesystem has and risking data loss.