Baker's Pure Rye 1847
With any collectible spirit or wine, it's important to verify the seal. A tampered seal could mean the contents aren't original. But all that was sealing this bottle was a lone, “naked” cork. No foil capsule, no tax strip, no laser-etched tamper-resistant cap… well, you get the idea.
Fakers use new corks and dirty them up to look "old." Or they recycle an old cork... poorly. This cork exhibited all the classic shriveling and "crud" patterns that experts look for. But why was there no capsule, no covering seal of any kind?
19TH CENTURY WHISKEY BOTTLES & CLOSURES
Whiskey from this era isn't supposed to have a capsule, or any other kind of closure. A driven cork is all we expect to see. Screw caps, crimp caps, and fancy whiskey seals (and even unfancy ones) were still many decades away.
This whiskey is so old that the mere fact it was sold in a bottle made it special.
Bottled whiskey was rare before 1870. Glass bottles were individually hand made and expensive. See that illustration on the left? That's from a book explaining "modern" glassmaking techniques -- in 1884. This bottle was made three decades before that! Bottling lines at distilleries were unheard of.
Instead, distillers sold their barrels directly to wholesalers and retailers. Then you, as a consumer, would bring your earthenware jug to your local merchant (or they'd give you one), and they'd fill it up with the product of your choice. Or, you could fill up your demijohn (a big multi-gallon vessel) and keep that at home, pouring it off into flasks as you drank it down over time. Which back then, often wasn't that much time.
So, this was a high-end whiskey for the period, gleaming in its own custom-labeled, brand-new glass bottle. A wrapping over the top would've been unnecessary, and actually purposeless. 
THE CORK’S CONDITION AND DEGRADATION
Experienced collectors know that whiskey can and does evaporate right through the cork. That’s why the level of this bottle was already a bit low (although it was at an outstanding level for its age). In order to stop that evaporation, collectors will often cover the seal with a non-damaging, non-permanent, airtight wrap.
But the problem with this bottle wasn’t just stopping evaporation. It was stopping the cork from falling into the bottle altogether. It had sunk dangerously low, sadly in large part due to changes in storage and environment when it arrived in California.  There was no telling what could happen next. Literally. Nobody could tell.
I spoke with whiskey experts, wine experts, and cork experts – everyone had ideas, but there was no precedence for something like this. Because nobody has experience with corks on 150+ year-old, full whiskey bottles. Because there aren’t any to gain experience with!
To wine experts, the solution was obvious: recork it. This is sometimes done with vintage wine in a careful and documented way. But in the spirits world, recorking is virtually unheard of.
But in this case, it wasn't just the best solution, but inevitable.
To verify the whiskey, samples had to be pulled for lab analysis. The process typically relies on a syringe, and the cork “healing” afterwards. But nobody knew how this ancient cork would behave after the seal was breached, and it was nearly certain to become compromised. If left on the bottle afterwards, the contents would die, too.
Guinness was the final party to give their approval, and then it was official: samples would be pulled, and the bottle’s dying cork would be replaced with a more reliable and safe closure to protect the delicate spirit inside.
 To really understand this, recognize that this was way over a century before product tampering became a common concern in general, and decades before refilled whiskey bottles were an issue. An 1850's whiskey consumer would've trusted their whiskey merchant similar to the way we trust pharmacists to properly dole out a big container of pills into smaller, non-sealed vials -- or in the way that a simple layer of Saran wrap around a cheese wedge doesn't make us doubt that wedge actually came from one giant, branded cheese wheel that the grocery store originally received.
 Upon arrival in LA, the educated consensus was to stop evaporation by covering the bottle's top with a thick layer of Parafilm. This was especially prudent since there were no labels/seals for the Parafilm to damage. That decision proved to be faulty, although ultimately irrelevant. It was faulty because while it did prevent further evaporation, it changed the "environment" of the cork enough that the cork realtively quickly (over the course of less than a year) receded down into the neck, whereas it had previously been mostly flush with the lip. Nevertheless, this was irrelevant, since samples needed to be extracted, and extraction would require replacing the cork in whole.