What happened here is what always happens with all printed and digital material that goes through some evidentiary process.
The shot-callers demand the material, which is a task fobbed off onto some nobody intern who doesn't matter (deliberately, because the lawyers and career LEOs don't want any "officer of the court" or other "party" to put eyes on things they might need to deny knowing about later.) They use only the most primitive, mechanical method possible, with little to no discretion. The collected mass of mangled junk is then shipped to whoever, either in boxes or on CD-ROM/DVD (yes, still) or something. Then, the reverse process is done, equally badly, again by low-level staff, also with zero discretion and little to no technical knowledge or ability, for exactly the same reasons, to get the material into some form suitable for filing or whatever.
Through all of this, the subtle details of data formats and encodings are utterly lost, and the legal archive fills with mangled garbage like raw quoted-printable emails. The parties involved have other priorities, such as minimizing the number of people involved in the process, and tight control over the number of copies created. Their instinct is not to bring in a bunch of clever folk that might make the work product come out better, because "better" for them is different than "better" for Twitter or Facebook. Also, these disclosures are inevitably and invariably challenged by time: the obligation to provide one thing or another is fought to the last possible minute, and when the word does finally go out there is next to no time to piddle around with details.
In the Epstein case, the disclosures were done years ago, the original source material (computers, accounts, file systems, etc.) have all long since been (deliberately) destroyed, and what the feds have is the shrapnel we see today.