I'm worried about my Windows apps modifying the files in Ubuntu, as there is software in Windows that can see and can modify files on the Linux partition. Can files or applications run normally in Ubuntu after modifying? If so, how can I watch the files for changes in Ubuntu?
Altrough you question is ambigous, I will give you a method to monitor your files.
If you want to see the list of files modified you can use the
for example, in this case those modified in the last 1 day.
In general, yes, files on Ubuntu will be fine if they're modified in a way they're intended to be, even though it's from Windows. For example, editing an image with Photoshop.
However, there are a bunch of little exceptions, and the only way to find out for sure is to experiment:
Most of these issues aren't tragic and can be easily corrected or worked around. But they're things to keep in mind.
My advice: don't go through the hassle of multi-boot situations. Just get a second computer (a cheap one if necessary) to run the other OS on. Or, boot another OS in a virtual machine.