This seems less of an issue, and more the need for regular maintenance; you know, that thing that everyone knows about, but never wants to do. 
Related: I recently wrote [Primer] NTFS on Linux which might be a useful reference when dealing with NTFS volumes. It also includes several notes that are relevant to a multibooting scenario.
This is always my recommendation; use separate disks; rather than attempting to squeeze every OS onto the same disk. Keeping each OS isolated from others (as much as possible) both minimises the associated risks and makes for easier removal (or replacement) of an OS, should it ever be necessary.
That said, sometimes a separate disk is out of the question (most Laptops), and one sole, solitary disk is the only game in town. A one-disk-multiboot is manageable, however, only if careful thought is given from the onset and each OS is setup to not interfere with the other.
Unfortunately, the majority seem to setup a multiboot with an ad-hoc ‘Each OS is installed, they should just work, right?!’ attitude. 
- There is a right way (and a wrong way) to do most everything.
Many people do indeed seem to treat an OS (and a computer just like their cars: they know all the knobs and switches; how to kick the tyres; light the fires; they know how to drive (mostly); but when it comes to changing a tyre they throw their hands up in the air and run about like a headless 
until someone else does it for them.
I know several people like that. I’d just tell them… ‘Catch a bus!’. 
I consider myself OS-agnostic; but with ongoing reservations.
I’m part way toward completing a Guide for multibooting Linux and Windows on the same disk, if that might be of use for you. It will be a few days (or so), before it’s published.