You can have as many files open as you want(*), in fact, by default your application will already touch a bunch of files just from being opened. It's not uncommon for larger applications to have 50+ open file handles at the same time, so no, that's definitely not the source of your problems.

I would argue you should see about finding the bug in your code that is causing the data corruption. Chances are it will also show up with just one file open, just with a different configuration. And if that's not enough, keep in mind that NTFS is a horrible, horrible filesystem that uses one big lock so every filesystem access is extremely expensive. Definitely not something you want to do in real time.