So the new version of Audacity does not play well with FAT32 formatted drives, which probably includes your SD card.
For some insights as to why, see here.
As for your original .aup file, be sure that that file and the associated directory are both contained within the same directory. You should have “MyProject.aup” and “MyProject_data” together in the same directory. If you have renamed either of them or both, rename them back.
I hope this helps. 