Apparently, GitHub stops indexing repos that have not had a commit for over a year. They say this is to ensure that search limits itself to providing the most relevant results.
But this is a pain if you know your own repos contain some particular information but GitHub turns up no search results because of this constraint.
A way to force a reindex of a repo is to search it - you may get no results but GitHub will put the repo in a queue to be reindexed and in about 5 minutes the same search may produce a result if the repo contains the relevant term.
However, if you don't know the relevant repo and want to search all your repos, it's somewhat inconvenient to have to manually search them all to force a reindex.