when you merge the file are you just overwriting the same file or are you deleting the old file and saving it as a new file name?
when merging a scene file make sure you have the same unit set a you're previous scene, slowly merging one object at a time, keep merging you're scene file until you come to the last object if max does not crash then you know it's the last object that is cauing the problem, don't merage that one. you will need to remodel it.
then as i have said you would need to save it as a new file name and delete the old scene file this can be annoying, so always use the save as then it the plus + sign this will take another copy of you're scene file as a back up
as a last option you can delete. the max.ini file but i will not do this less you know what you are doing, once you deleted that max.ini file then restart you're computer and autodesk will replace that file