"I found two of my old Github repos in there. Both were deleted last year and both were private."
The Stack was constructed a while ago, so "deleted last year" wouldn't have an impact if it was constructed before then.
"Both were private" is the thing that needs to be unpacked here. Were these genuinely private repositories that had never been made public on GitHub?
https://huggingface.co/datasets/bigcode/the-stack-v2 talks about where the Stack comes from: "This dataset is derived from the Software Heritage archive, the largest public archive of software source code and accompanying development history"
You can search that here: https://archive.softwareheritage.org/browse/search/?q=simonw... - it would be interesting to know if the OP's "private" repos are included in that collection.