I'm a master electrician and I've seen this numerous times. IMO it is not safe. The quick fix (which I discourage) is to isolate both home runs at the panel, then disconnect the hot & neutral of one of them. This is still bad because now you have what's known as a back feed in the panel, and some poor unsuspecting inexperienced electrician could easily get the crap knocked out of them because normally power leaves the load center. It's a "shocking" surprise when you find a back feed. Furthermore, if either of the home runs are are 12/3 (shared neutral 2 circuit) you could create a 240V series circuit by disconnecting the wrong neutral. It's also possible that it was intended to be 2 circuits, so disconnecting 1 breaker could leave you with an overload. Parallel breakers do double the available current which is in excess of what the wire is rated for. Under normal operating conditions it's fine, but that's not what you care about when dealing with over current protection devices.
The right fix
Your electrician is lazy. Forever is a long time in a lonely place. You can sniff it out yourself in an hour or less with no special tools, beyond linemen pliers, strippers, a screw driver, and a test light. A jam box is a good substitute for a test light when working by yourself.
1st, turn off every breaker except for the 2 parallel breakers in question. Now wander around your house and map out all the lights and receptacles that are still hot. Assuming it's #12 wire on a 20 amp circuit, you should expect to fine 10 - 12 plugs and lights if it was supposed to be 1 circuit originally, or 20 - 25 plugs and lights if it were supposed to be 2 circuits. If the breakers are 15A and the wire is #14AWG, reduce those expected quantities by 20ish%. Now take into consideration if something should be a dedicated (solo) circuit such as a refrigerator, washer, etc. If that's the case, shut off the power, pull that plug, and disconnect 1 set of wires and cap them off with wire nuts. If it all appears to be general purpose, you're gonna wanna break the circuit somewhere in the middle. Typically one wires in a linear fashion, meaning you leave the panel and wire in a shortest distance possible, or room by room. Look at your map, I'd bet you see some sort of circle. Pick a plug at the furthest point from the panel, shut off the breakers, disconnect and cap 1 set of wires, fire up just 1 of the breakers and retrace your map. You're looking for balanced quantities, but it doesn't have to be exact. If you have 9 plugs on one circuit and 12 on the other, that's good enough. It's considered good etiquette to leave a note in a box with a dual feed where you've split the load.
If yo get cold feet, find a different electrician. If you want to do it yourself, but want more internet guidance, then go ahead and map out the circuit in question and post back with a diagram. I'll talk you through it. Take pictures. Approximately when was the apartment built? What is the wire and breaker size?
-Richard