I am not sure where they are in your design, however make sure Ref. Des. column have a check mark in Display Color Setup. Next assign different color to Ref. Des. for Top layer (1), Silkscreen Top (26), Assembly Drawing Top (27) and see where they will show up. The number I reference to are default numbers in PADS and may vary if modified them.
I tried toggling all of those setting and they didnt come back. I am getting them to come back by selection each part and adding new label to each one. Im not sure what i did to make them go away but im bringing them back 1 by 1.
you can select all the components which does not have refdes and you can generate refdes in one single step from properties-labels.
for the missing refdes, select a component(which does not have refdes) go to labels under properties and select a refdes which is already available in the dropdown list and check if the show is set "none" or "value". if it is set to "none" change it to "value" to get you refdes back.
We also see this error from time to time.
We haven't figured out exactly why this error occurs, but sometimes it seems to occur if the 'BaseOption' in Assembly Variants for some reason get all the components marked as 'Not Installed'. I know it sounds weird by that's the closest we can get to the cause for this error.
Sometimes it can be solved by just closing PADS Layout and reopen it again. Other times we need to add the RefDes labels by using the slution described by sravankumar.padarthy.