Are you working with form presets? or actually saving the form as a php file?
I could see what you are describing as happening when working with form presets. It sounds like you are saving a preset of the contact form, then editing the preset, removing some fields and saving it again overwritting the first preset.
the save as preset dialogue box will give you the option to rename the preset. If yoou use a new name, it wont overwrite the previous preset.