We are currently moving over courses from a 1.9 site to a 2.1. We are noticing that the course "files" in the 1.9 site, that were not linked to the moodle course, but instead where just under "files", are not showing up. Where would we be able to find them? We do not see them under server files.
How are you managing this migration? If you are just trying to move things via the moodledata folder then you are asking for trouble. The entire database and moodledata structures are setup very differently.
Your best bet is to create a duplicate of your v1.9 Moodle, database and all, then delete out of that any third party blocks and so on, anything that is not Moodle core, then upgrade. Delete the v1.9 code, but keep the config.php file, then paste over the extracted v2.1 code and then open the Moodle. All things being equal and with a bit of good fortune, it should all work first time. The new database structure should be generated without wrecking your existing database, and all data should be preserved. Once you are satisfied your system is working, you can then FTP the new Moodle back to your site, change the config.php file, and run the replace.php file to update the internal links. This method doesn't cause too much anxiety and leaves you with a perfectly good test bed so you do not have to worry about harming your site when you want to upgrade or add in blocks or make other changes. Test it on your test bed first, trial it and when happy, then you can smoothly update your production site.
Thank you so much....The Legacy Files is working great!