They're separate, separatte file systems, separate partitions, and where does this 'fear' come from.
If you're really paranoid do full drive chkdsk and run vendor's own utility to map out and test/format, definitely don't use or rely on Apple to zero-all a drive. Or use another 3rd party tool before you commit data or file system or OS to any new drive. Then do same once a year.
You aren't moving partitions. Files on NTFS don't have anything to do with HFS.
And you can easily run chkdsk as needed on NTFS. Not so with HFS.
As for the rest, put in place a better backup and system repair and maintenance routines.
I think Windows runs one automatically on weekly basis, and that seems to be about right.
NTFS is affected differently. HFS deals with different types of file and space fragmentation.
Diskeeeper even helps avoid NTFS fragmentation problems, especially HyperFast which is used with SSDs.
Files are always being written and when updated they don't go to the same block anyway (read, write temp, lock, delete original, unlock).