Whenever I link any object from another .blend file (happens with all .blends, not just one) in 0.3.5 and hit P or use Blenderplayer, the linked object will disappear and be unusable in the player. It is invisible, has no physics, no logic or anything. I tested in UPBGE 0.3.6 and linked objects work as intended there.
However, UPBGE 0.3.6 has the app-breaking bug of crashing every time you weight-paint on macOS - this interestingly went away when I switched audio to OpenAL while in Weight Paint mode, but again started when I switched back to Object Mode and then switched to Weight Paint mode and clicked the cube again to test and it crashed. The weight paint operator which handles switching the modes also handles weight painting, and for some reason on macOS, generates a Python backtrace/exception or something else which causes UPBGE 0.3.6 to crash on macOS, likely due to some code which got screwed up in the process.
Back to linked objects, the linked object(s) are still intact when I exit the game - it is not deleted from the scene or collection or file. It seems like a bug in 0.3.5, as it affects the ones that are Instanced. I tried resetting UPBGE 0.3.5, but that didn’t do anything either. This seems like a collection problem when UPBGE 0.3.5 grabs the collection from another .blend file and links it to your main .blend file.
This is definitely a bug by all means.
The weight painting bug in 0.3.6 on macOS that causes the app to crash is much more serious, and should be looked at and fixed immediately. I hope that one gets fixed in 0.4.0, as that makes 0.3.6 unusable for me.
The bug with linked objects in 0.3.5 means I can only link objects by not instancing it which is where this bug does not happen, which therefore means that all editing of that object is locked, and this I don’t want to do. Most people will link objects as it is easy to do, so why is UPBGE 0.3.5 not seeing any of my linked objects in any file when I push P or use Blenderplayer?
If any devs see this, please consider fixing these two bugs or provide some help on how I can work around this linked objects bug. It’s only in the player that the linked objects disappear - the linked objects are intact when not playing. I cannot report bugs on the developer forums as you require an account to do so, so I can only do it here.