I don't have a Magellan, so this info. is is of a general nature. The 'internal' battery in GPS's is commonly used to retain some or all of the following :- Waypoints, tracks routes etc, the almanac (a record of which satellites should be in the sky), the time and date. The kind of problems that can occur if the internal' battery fails are:- loss of Waypoints, tracks routes etc, inability to know what the current time / date is resulting in an inability to 'find' satellites and having to re-learn the almanac resulting in satellite finding taking much longer, if at all. Some internal batteries are re-chargeable and are charged by the main batteries, however, even re-chargeable batteries can only be re-charged so many times before they fail, other internal batteries are not re-chargeable and obviously eventually run down. I would say that if waypints are retained when the main batteries are removed for any length of time that the internal battery is O.K., however there are other things that can go wrong, your GPS has an internal oscillator which can 'learn' the true frequency it is supposed to be running at when it contacts the satellites, however if the oscillator has drifted too far out, it won't find the satellites in the first place.
Questions:-
Does your GPS display the correct time / date?
If the GPS's time / date is incorrect, can you manually set it?