As of a couple of weeks ago, Bundlr was missing the indexing of some transactions on Arweave causing them to drop from GraphQL query after a set amount of time (though they were still saved to Arweave). Issue here
Larger files (>100MB) have had trouble saving to Bundlr. This issue has been raised here and I've spoken to one of the engineers who says they are pushing out a fix (this is a Bundlr js-client issue)