I am just curious ... were they 70k payments entered manually over time, or were they imported or added via some sort of application in bulky chunks?

They were entered manually over time, none have been applied since 2018, all different customers. 

They were entered manually over time, none have been applied since 2018, all different customers. 

Not that this helps you now, but both AR and AP have payment explorers and reports.  To monitor going forward, perhaps a report / explorer should be run periodically looking for an unapplied amounts <> 0.  As I am a technical person and not a business user, perhaps others can comment on how they prevent unapplied amounts for getting out of control.  

Also, both AP and AR have an option to warn about unapplied payments during document entry.  If these options are not checked, then perhaps you may wish to consider checking them.