Is it safe to manually delete the contents of the .Trash-1000 folder on my SDCard?
.Trash-1000 is a metafolder like Windows's Recycle Bin, normally created by Ubuntu (and perhaps other Linux variants).  Have you deleted anything on your SD card from your PC?  That would explain it.  You can safely delete it.  See also: https://superuser.com/questions/169980/what-is-trash-and-trash-1000