Miltoniopsis with spreading brown on pseudobulbs
 

This Miltoniopsis came to me on August 24, and when I opened the box, the roots at the base of the pseudobulbs were black. The plant itself seemed all right, but everything that was a root was either black or brown and mushy.
I don’t know if this happened in transport.
In retrospect, I should have called the seller right then.
I treated it with Physan 20, cut off everything that looked rotten, and repotted it in LECA.
I sprayed it with hydrogen peroxide, I cut off some growth that looked bad, then applied cinnamon to the cut.
Fast forward to today: there are these brown spots that keep getting larger and they seem to be spreading to all the pseudobulbs.
I am not sure whether to cut these off or try to treat them.
Any advice would be appreciated.

I can't see the bases of the pseudobulbs, so I can't see the discoloration you mention. If the bottom of every pseudobulb was mushy and brown or black, the plant was dead on arrival.

Even if it were healthy, you've planted it too deeply. The bases of the pseudobulbs should be at the surface of the LECA. You've almost completely buried them. It is often necessary to stake newly-repotted orchids so they don't fall over, until they grow a new root system that grips the medium.

You don't say where you live. Miltoniopsis don't tolerate much heat. They are difficult for most people in the US to grow because conditions, even inside the house, are too warm for most of the year. If the box was left in the sun for more than a few minutes, or if it was left in a warm place in transit, the plant could be killed.

That isn't enough to tell. I can't see the pseudobulb bases.

Well, I pulled it out and every single base was affected.

Lesson learned: do not purchase this type of orchid via mail when it is hot.
I could have grown it. My house is 72 and I have a cold room that stays 66.