Depends on the charger. And the batteries
The best chargers will always charge each battery individually. This is OK
The cheapest chargers (overnight ones) just trickle charge the batteries for hours and hours and hours and they'll be as OK as any other battery setup.
The medium grade chargers charge in pairs and they'll likely screw things up.
Also, the "rated" capacity and actual capacity are often very different. So you might be OK because your 2000mAh and 2500mAh batteries are actually fairly similar batteries that just have different ideas of what the "mAh" part really means. And/or have been worn down differently.
No easy answer. Batteries are trouble.