When you load up the backups of different wallets, I recommend running bitcoin with the -rescan option. This will tell bitcoin to ignore how much the wallet "remembers" having and recheck how much it actually has. This way, you don't even have to worry about any of the issues you bring up.
To use the rescan option in windows, alter the shortcut to have -rescan at the end, or open up the command prompt and run the .exe with -rescan at the end.
The problem with the person you mention has nothing to do with the fact that the the coin "had no where to come back to". What happened is that he added a new address to his wallet, and sent the money to that new address. But he didn't back up a file that contained that new key and deleted the new wallet. So he lost the key forever. As long as you send the money to an address you know you have control of, and DO NOT DELETE ANY WALLETS, you should not have a problem consolidating your funds.
Here is what he did:
Made a wallet with one address
Backed up that wallet
Added a new address to the wallet on his hard drive
Sent all the money to that new address
Deleted that wallet on his hard drive
Loaded up his backup that only had the key for the first address not the new address
The main mistake was deleting the wallet. Don't delete any of them, that is the only way to mess up.
EDIT: This wasn't completely his fault, since wallets are suppose to create 100 addresses for you to use, so the second address should have been in the backup, but there was a bug. Still, it would have never have happened if he didn't delete the wallet.
so how do you organize all these extra wallets?