So I have found that no matter the size my eggs are, the yolk will always be the size it is suppose to be. This is great when you have pullets laying "fart eggs", because I love yolks but whites not so much. However, these eggs do run a higher risk of bacteria entering into the egg and the yolk, as the yolk is for sure touching the shell which can increase your risk of bacteria infecting your eggs. This is why many people store their eggs smaller side down, so the yolk floats up to the large end where it won't touch the shell.
Am I reading this right that the egg was on the counter for months? I wouldn't leave an egg on the counter, even with an intact bloom for longer than 2 weeks. Especially not one where the yolk is very obviously touching the shell.
If you are worried about your chickens health it doesn't sound like something as serious as a lash egg. As long as this is just something she does occasionally, these odd things do happen.