Hi Elisa,
Thank you for contacting us and I'm sorry about the issue you are experiencing. I'm not sure I understand your issue here exactly. It sounds like you are having syncing issues that are causing you to lose information? After restoring from a backup file, mSecure 5 will clear out any previous information from your local device, our system, and any other device before replacing the information from whatever is in your backup file. I'm not sure what you mean when you say that you created a backup of mSecure and stored it on iCloud. Can you let me know what kind of backup file you have? What does the file end in? Does the backup file end in .msim or .msib? Did you create the backup file through our email backup option or through our internal "Backups" option? How are you restoring your information? With more information, perhaps I can understand what might be causing your issues here.
Elisa