Bad news can be turned into useful news ----- for the future, that helps us all.

It is possible that the roots were damaged during the repot. But - even though not absolutely sure - it's also possible that those particular roots could have drowned - being in too watery conditions in the media. Hard to say.

The nice thing is you unpotted to get an idea of the situation with the roots. That was good.

If an orchid has heaps of roots that had grown in the pot, and then the plant gets transferred to new media, then it's important to have a rough idea about the state of the media and the roots when watering the new pot and media combination.

If a pot is filled with lots of media - and if that media combined with lots of water is able to create very watery or sludgy or soggy/soppy conditions for relatively long periods of time - and taking too long to become 'lightly moist' or 'lightly damp' again ----- then regular roots of orchids can take a nasty dive in health. Probably due to oxygenated water not being able to move around quick enough down there in those dark depths.

One test or check can be to have a similar pot with similar media --- with no orchid. And if you water in the same way - same schedule, same rate, same amount ----- same as if you were watering a potted orchid -- then after a week or so --- check the media by digging down into it .... to the middle and bottom of the pot.

If the media is really soppy and wet ----- then that can be an issue. It depends on whether the roots are adapted to that sort of condition or not.

Sometimes, a combination of cold and wet for long times is a problem too.

Is it normal to even be seeing the smaller new leaf at the bottom and top leaves to be yellow?

I have increased watering but see no improvement.

Alas, this does not look good. Especially the yellowing of the top leaves. The crown may have already died. If that is the case, if the roots are good there is the possibility of a new basal growth, so don't dump it.