The creator of tildes.net is a former Reddit backend developer, and believes this behavior is likely due to how Reddit caching works (or doesn't work), rather than an intentional subversion of user intent:

Yes, this is almost certainly a technical issue. The way reddit caches things probably isn't the standard way you're thinking of, like a short-term cache that expires and refreshes itself. There are multiple layers of "cached" listings and items for almost everything, and a lot of these caches are actually data that's stored permanently and kept up to date individually.

For example, when you view your comments page, Reddit uses a cached (permanent) list of which comments are in that page. There is a separate list stored for each sorting method. For example, maybe you'd have something like this with some made-up comment IDs:

Deimos's comments by new: 948, 238, 153
Deimos's comments by hot: 238, 153, 948
Deimos's comments by controversial: 153, 238, 948
If I post a new comment, it will go through each list and add the new ID in the right spot (for example, in the "new" list it always just goes at the start). If I delete a comment, it goes through every list, and removes the ID if it can find it in there.

One of the problems with this system (which is probably what's causing @phedre's issues, and affecting many other people trying to delete their whole history) is that all of these listings are capped at 1000 items. If you already have more than 1000 comments and you post a new one, the 1000th comment currently in the new list gets "pushed off the end". The comment still exists, but you won't be able to see it by looking through your comments page, because it's no longer in that listing.

Deleting comments also doesn't cause previously "pushed off" ones to get re-added. If you have 5000 comments, your listing will only include 1000 of them. If you delete 50 of the ones in the listing, your listing now has 950 comments in it. If you delete all 1000 from the listing, your comments page will appear empty, but you actually still have 4000 comments that will be visible in the comments pages they were posted in.

And this is only one aspect of it. There are also multiple other places and ways that comments are cached—comment trees are cached (order and nesting of comments on a comments page, for all the different sorting methods), rendered HTML versions of comments are cached, API data is probably cached, and so on.

All of these issues are probably just some combination of all of your posts being difficult to find and access due to the listing limits or certain cached representations of posts not being cleared or updated properly.