You may currently be experiencing an issue where the comment count on a video's watch page is different from what you see in YouTube Analytics. We're updating our systems to ensure consistency, so the numbers may have recently changed for you.
Rest assured that even if your comment count has decreased, no comments have been deleted. YouTube never deletes comments unless they violate our rules for spam or other policies listed in the Community Guidelines.
What's the correct comment count?
On the watch page, the actual comments loading on the page is the accurate number. The number that you see listed above the comments field on a video's watch page may not currently be accurate.