@Tim Edwards when extracting from gds using

extract unique notopports

, how does magic recognize the top cell? Is it the cell that is specified in

load cell -dereference

? Is

select top cell

needed? I’m seeing lower hierarchies with non unique ports (unconnected nets with the same text) being extracted as connected. Wanted to make sure I’m not missing a setting before creating an issue.

Whatever cell is the edit cell should be considered "top"; however, I wouldn't swear that

select top cell

isn't required because the command syntax is a bit irregular about which commands act on the current edit cell vs. the cell currently in the display window, which need not be the same thing.

I’m doing everything in batch. Does

load <cell> -dereference

make

cell

the edit cell?

Yes, it should. I'm guessing that you're seeing a real bug and should create an issue.