i just tested this by adding a scene ("0010") to a project called Hover* and experienced the same (WIN10).
i followed
this advice for
similar IDE issue and the new scene stayed visible on re-launch.
it's not the most eloquent solution where it will reset
everything but it worked.
*since the reset, i went into agkide.layout and found these 2 entries for Hover:
[Window][main.agc##Hover.agk]
Pos=385,72
Size=1149,723
Collapsed=0
DockId=0x0000000D,1
[Window][0010.scene##Hover.agk]
Pos=385,72
Size=1149,723
Collapsed=0
DockId=0x0000000D,0
note the Dockids (0,1).
i added another scene "0020" and checked the .layout file and found:
[Window][0020.scene##Hover.agk]
Pos=385,72
Size=1149,723
Collapsed=0
DockId=0x0000000D,2
ie, id = xxxx,
2
so, i wonder if you can get yours to show (without the "hard" reset above) by building a similar entry in the .layout file (keeping everything the same as the ##ProjectName.agk but making it XXX.scene##ProjectName.agk) instead and increasing the dockid by 1 (may not even be necessary. i wonder what the IDE would do if it was the same)? reset itself?)?
otherwise, deleting the .layout file alone (vs the whole folder) might do the trick where we could probably save the other stuff (agkide.ini, layout preferences, etc,) while fixing this/similar?
---
add: i re-read your post and realized that i didn't answer your question, "Can anyone advise what I'm doing wrong?"; i don't know that you
did do anything wrong. sorry about that.
meanwhile, from the user guide @ Preferences/IDE:
Only Display Active Project Files
This is on by default. If you tick it off then all the files from the projects list will be displayed at the top of the IDE in tabs.
i'm not sure what "active" means. only the one that's currently being worked with? regardless, ALL scenes that are added to a project, whether created anew or brought in via Add File
should show in the project window.