I have a dual boot setup and when I booted into windows one time chkdsk automatically ran. It ended up deleting a bunch of files on my NTFS storage HDD, all the deleted files were created on Linux. What's the best way to go about recovering the files? And how can I avoid this in the future?
Sorry I can't help you further, except to speculate that something corrupted your files before Windows chkdsk got to them - whether an unexpected power loss or something you did to the drive, ... I have no other ideas.
For recovery maybe try testdisk (to see if they can be undeleted) or photorec (otherwise).
You can get both from http://www.cgsecurity.org/