We're currently running into a very strange issue wherein a certain group of files (linked into our local Galaxy instance and accessible via "shared data") can't be previewed or downloaded once they're imported into a history. If one tries to directly download these datasets via "shared data" then everything works and the resulting tar.gz files contain everything they should (and can be opened and the file contents match what's on the hard drive). To test if this might be some group/role permission problem (though I still personally have the same problem when I login as an administrator) I've tried making a few of the files public, but that also doesn't seem to resolve the issue.
So, in short, Galaxy seems to be able to see and access the files without issue, but something unexpected is happening if and only if one tries to interact with the files once they're in the history. I'd be more than happy to play around with the python code if needed to try to track down the source of this, but I'm hoping that someone has other suggestions :)
Before someone asks, no, this weird issue doesn't generally occur with files that we've linked in, just with a single recent dataset.