Give the handler company baggage tags (or alternatively use the handlers' tags...they do have them!), have them write the Aircraft Tail Number, airport of departure and destination on each tag and tag each bag.
Alternatively if you're in a situation where you're at an airport where the folks drive straight to the plane from their palace, tag each bag as you haul them onboard.
Count each bag as they are loaded, take note and when you arrive at your destination you can say "20 bags were loaded in JED for this group, 20 were offloaded for the same group...Look, they have tags!"
That's what we do... Sometimes :-/ ...not perfect by any means but at least it looks like we are doing something.
It's a near impossible task in this industry, especially when the bags arrive at the airport ahead of the pax. You're never going to know who they belong to, nor are you ever as most of the passengers are just going to get irritated if you ask them to identify their bags.
In our security manual we have it written that if there is a chance that an extra or unidentified bag MAY have been loaded onto the aircraft, the bags will be offloaded onto the tarmac or onto trollies and each bag must identified by each passenger. That's the only time we state there is a requirement for the pax to identify their own bags.
Good Luck
DB