Re: automation and deleting tracks...
This could be because of your automation pref settings. Your choices are Always, Ask, and Never. I'll bet you have it set to "Always".
Let's say you're comping vocals and you have three tracks with various takes on them. They're all assigned to the same audio channel (e.g., three tracks of Audio 1). Automation written on any one of those tracks will appear on the others as well. This is because automation is not track-specific; it's channel-specific (in this case, Audio 1).
With that in mind... with prefs set to "Never":
Say you deleted all of the regions on track 2 and 3, leaving regions only on track 1. Automation will not be deleted in the vicinity of the regions. And deleting unused tracks at this point will just eliminate tracks 2 and 3 and nothing more.
With the prefs set to "Ask", Logic will ask you to if you want to delete the automation. You answer yes or no.
With the prefs set to "Always", deleting regions (or tracks with regions on them) will, depending on a variety of conditions (too many to list), wipe out the automation. Under certain conditions you will be warned first.
So check your [b]Prefs > Automation > Move Automation with Regions[/b] preferences for the best setting for you.