lost attachments on upgrade - why & what to do?

I upgraded from Drupal 6.13 to 6.14 using Fantastico and lost all of the attachments. The links to each of them was still on each page, however clicking it would result in a “404” Page not found” error. Fortunately I had made a copy of the site and went into it and copied the attachments in “sites/default/files” to the equivalent folder on the main production site and everything behaved as it should again.

My questions are whether this is typical of what I can expect after any upgrade, if this is a Fantastico glitch that would not occur if I upgraded otherwise, and if there is perhaps a better way to manage this problem.

I am afraid that I seem to be managing Drupal reasonably well and coping, however I don’t know much about what is going on behind the scenes.

Thanks,

Ray