

Delete windows partition with your preferred tool and update-grub
should remove the item from boot menu. Then, depending on your partitioning schema, you can either create a new partition in the empty space and mount it however you like or expand your existing linux partition, but options there depend on how your partitioning has been originally built and if you can leverage things like LVM or ZFS when expanding the usable storage.
And, while pretty obvious, make sure to only delete the correct partition and all data stored on that will be lost, so make sure you don’t have anything important on windows side of things.
Someone with more experience on sed or awk should chime in, but out of memory something like this (which MOST LIKELY WONT WORK, verify it before running it on anything important):
find -name *mkv -exec sed -e's/file=.*/file=' > {}.changed \;
That, at least in theory, reads every .mkv file recursively in a current working directory, finds lines that contain “file=<whatever><EOL>” and replace that with “file=<EOL>” and stores the output to <original filename>.changed.