Yes, that can happen for any number of reasons.
Unless you have a non-standard setup, you should be able to reproduce this:
blk0001.dat blkindex.dat database/ db.log debug.log peers.dat wallet.dat
There's your wallet, the wallet.dat file. Strictly speaking, you don't ever need to copy it back in to ~/.Mintcoin, you can restore within the wallet from a backup explicitly saved in , say ~/Documents/backupwallets/.
To get Mintcoin working again, first copy the wallet to a safe place then you can delete everything in that directory other than the wallet and start the MintCoin app again. Can't promise anything after that but the Ubuntu aspect is fairly standard, ~/
~ is unix for $HOME; cd ~ and cd $HOME are the same thing.
HTH
Cheers,
Graham