The scripts only work from your profile, specifically it checks the New, Hot, Top and Controversial pages. Each of these lists (and some of them let you sort by time also) are limited to 1000 comments.

If you have an old account with lots of comments, you may find many of your comments don't fit into these lists, and won't have ever been deleted by the scripts. For myself, I kept a link to a couple of my old Top comments open, ran the script, then found the top comment had been deleted but my subsequent replies (old comments with small karma) were left untouched.

The only effective way to get these comments is yo use the direct comment links in a data access request. This data can be fed into some scripts, eg shreddit (the github version not the paid website version) and can automate it, however I'm not sure if these still work since 1 July.

As for comments being restored, supposedly this was because of reddit's CDN structure. You'd delete it on one node, then another would restore it. This did not happen in my experience when deleting via the direct comment link, rather than from the profile pages, and I haven't had any restored since the end of June.

That’s not what’s happening here. I have used a script (not this one), it went through all my comments, overwrote them, and I checked my reddit profile and it was all gone.

Then, several days later, some comments were back again.

I ran the script again to delete those, and again reddit showed me that, in fact, they were gone. Only to have some of them reappear later… I think I ran that script about four times.

Now, I’m not saying this is intentional, because there was no rhyme nor reason which ones, though all of them were older and older every time I ran the script. I guess something in the backend of reddit isn’t working as intended, but it is, as a matter of fact, reddit who has copies of your comments and edits and reinstates them.

You should be able to Google search your username if you haven't deleted your account.