I have a design which I completed in December 2021 using version 5.99. It is a 4 layer board with footprints on top and bottom. It works OK so I am fixing it. 
Really I first designed it based on using parts that I have. But if I had to buy all of those parts then it could be done cheaper and that is what I am doing now. I have changed maybe 30% of the schematic diagram. I am now using version 6.04. I am about done revising the schematic and am now working on the pcb layout.
What has happened is that the pcb file lost the layout information for a big piece (a bunch of discrete parts) of the design which has not changed. All of those parts (I think they are all on the bottom side of the pcb) now look like new parts which need to be connected in the layout. So this tale of woe is not a big error, but rather I have to re-do a big portion of the layout which I had already done in the older version.
I think I had been trying to revise some of this discrete circuitry with LM339 comparator sections. But I decided that this did not work so well, so I opened up an older version and copy-pasted that section of the schematic in order to revert to that original portion of the schematic design.
So this is a minor pain…I am just wondering about any comments or suggestions? What happened? Did I do something worng?