Replying to @bikedeb's post:
I want to add a bit to the trevort's post. You need to consider that there can be 2 types of Backups - 1. backups that 'appear' automatically (i.e. a software makes them itself), and 2. backups that 'appear' manually, i.e. when the software does not interfere in the user relations with the application, and the user creates and keeps backups himself.
iBearMoney does not have automatic backups because we want the users to have full control over what they do. But I assume that you expect the Backup to be automatic, so that if you delete something, there is still a backup that you can load back.
It is not so here. If you want to load a backup back, you need to create it first, and it will not change over time. It will not be checking your new records to copy them. Backup is a 'photograph' of your current state, and it is a permanent photograph so you should not expect it to know what you do after you took it. But you can make several Backups if you want, so to answer your question "I am assuming they are stored in the backup file, correct?" we need to know whether the backup was created before you lost the entries, or after. If you created it before, then surely it did 'photograph' everything, and you can restore them back. But if after, it just photographed that there were no entries, and thus you cannot restore them.
Now a few more words about your situation: you seemingly did not upload a backup file from the computer, but you did it from your iPhone. Backups (i.e. service files as I referred to them in the previous post) can be kept not only on the computer, but anywhere else, i.e. on a flash drive, in your mail, and on the iPhone itself. By default, they are kept in the iPhone, but we also allowed users to download them to desktop computers because many people want it. So I think you uploaded a backup directly from your iPhone to the Money app.
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The app will project your budget, but of course, based on the data that it has. So since it does not have some of the entries, it will not take them into account when projecting your monthly budget.
Please don't hesitate to ask more questions.