They don't seem to be doing it on bad faith, but I do think they should've asked for more info before deleting your post.
I don't know how Mastodon's backend works, but maybe moderators could have an option that, instead of deleting a post, puts it on hold until the fact-checking process is done, including giving the post owner the chance to comment?
And if they see that it was flagged wrongly, they just enable the post to be seen by everybody again.