This is definitely not a typical behavior for AllMyNotes, we have nearly zero reports of data loss, as our database engine has self-healing features, it can restore even files badly damaged by hard disk failure.
If the issue happens only after installing app updates, it has nothing to do with data loss, likely you are resetting your settings to default state and need to use menu item File -> Open to open your data file from old location. It can be the typical case if Portable edition is installed to new folder. Also, it can be the case for Desktop version if you have very strict file access permissions set up by your computer administrator, so that the new app version cannot read old settings. Even if do not know exact reason, File -> Open should fix your issue. Alternatively you can create desktop shortcut directly to your data file, and launch it (not AllMyNotes itself), so the issue will not happen anymore.