In the comment section of quesions or answers when a previous comment is deleted there should be an indication of the deleted comment where the comment used to be. Now it's hard to follow an exchange of comments if the comment a new comment is referring to is deleted.
In that situation you should flag the comment / post itself to state that is unclear and one of the mods can either:
a) remove that comment
b) reinstate the deleted comment
They're not really for ongoing discussions anyway, plus comments get flagged a lot so it's often easier for the mods to just delete the flagged ones if they look like they're not much use instead of having to go to the post and read through all the comments on all the posts trying to decide whether they're useful or not.
But comments can be undeleted if necessary.