When you click 'save as' below where you put in your file name and type of file you want to save it as there is a bunch of tick boxes, so you just ticked the 'layers' tick box (which gave you a yellow attention notice in any case) ... and voila!!! Everything is back to normal
so you need to check the layer option otherwise it will be one layer instead of the original layers
I do, as mentioned in my post, make sure it is ticked. That doesn't help.
it's possible the layered PSD image became corrupted and Photoshop is just loading the flattened composite.
I suggest resetting Photoshop's preferences, just to rule out a corrupted preferences file.
To reset the preferences:
Press and hold Alt+Control+Shift (Windows) or Option+Command+Shift (Mac OS) as you start Photoshop
This is a common issue and is caused by the checkboxes.
1. When you first save a PSD , it will have save layers checked
2. When you save as a PDF there is a warning - but the implications are easily missed
If you uncheck Preserve Photoshop Editing capabilities to widen compatibility then the PDF is saved flattened as you would expect, although the layers remain on your open document so you can still do a further Save As and save it unflattened if you wish
3. But there is a further "gotcha" (which is what the warning eluded to). If you now try to Save As a PSD you will find the save layers box has been unchecked and you need to recheck it to save with layers. If you do not check it - then it will save flattened
Note : This only happens if you uncheck Preserve Photoshop Editing Capabilities when saving the PDF.