I am concerned about creating so many different, individual files, but should I be? Is there anything wrong with making lots of files, possibly hundreds or thousands of small text files?
No. If it works for you do it this way.
If so, my question is this: Is there a way to rewrite data in a file without messing up the other information stored in the same file?
Only as long as the length of the data sets to be written is known and does not change. If you have changing data you need an extra layer of complexity, like using JSON, XML or something like that. As long as your first idea works out I wouldn't do that.
