Use Latest Backup vs. Back Up Now

The Backup section of iExplorer is displaying the data that is within an iTunes backup on your Mac or Windows PC. If there is already an iTunes backup for your iPhone or iPad on that computer that is more than 24 hours old, iExplorer will ask whether you'd like to Use Latest Backup  Back Up Now. The window will also display how many days it's been since you last backed up that iPhone or iPad. As the choices suggest, if you choose to Use Latest Backup (Mac) or Dismiss (PC), iExplorer will load the previous backup which will be a snapshot of your device from over 24 hours ago, and if you choose to Update Backup (PC) or to Back Up Now (Mac), iExplorer will create a new iTunes backup which, in most cases, will overwrite the old one due to how iTunes is designed. 

If you'd like to create a new backup when the last one is less than 24 hours old, you would need to do so manually by right-clicking on Backup in the left panel and choose to Back Up Now (Mac) or Refresh (PC). 

Before choosing to Back Up Now or Refresh, if you have deleted anything on your iPhone or iPad since the last backup, be sure to use the Export buttons in each section to make copies of your data outside of the iTunes backup since iExplorer, the app itself, doesn't store any of your data and acts more as a window showing what's in an iTunes backup or what's currently on your device. The article below explains about this more in detail and will help you avoid losing any of your data:

How to keep a safe backup with iExplorer