So this is an issue that I've had for a long time and have just learned to deal with it thinking of it as a quirk of SolidWorks. But I figured I'd shoot the issue here in-case anyone knows of a way to prevent this from occuring.
Whenever I make a change to my models regardless of where in the model stuff is changed, I will have random centerlines disappear on the drawing. There seems to be no rhyme or reason to which centerlines disappear just that some do. For instance I make changes to a patterned component and say I have 6 of the part all with centerlines in the drawing. It's not that all centerlines will disappear or base will disappear and patterned will stay or vice versa. Instead randomly the 3rd will disappear or in other cases the 5th. Also often for the centerlines that disappear a new one cannot be added in it's place with the centerline annotation and I either have to select two new edges that would create the exact same center or draw in a centerline manually.
I've kinda learned to expect this issue and have just always made sure before I send out any drawings to verify that all centerlines are present and accounted for just I'd prefer if I didn't have to constantly regenerate centerlines. Any insight into why this happens would be most appreciated. Just for reference my version of SolidWorks is 2012 SP2 if that helps at all.