I've been having this issue since I began my time with the GMS Beta. By now, I expected this to have been talked about and resolved, but as of now, I seem to be the only one with this issue. What's worse, since I have no idea where these issues have appeared, and thus I feel I would be obligated to share the project this is occurring in, which I am unwilling to do.
Every single time I load into said project or run it, a small dialogue from the Output saying "Blank IdReference Found - could be that the project is corrupt". I have had no signs of corruption of the games files except for one event where the project had corrupted itself when imported from Beta v7 to Beta v8 (thankfully I had a backup at hand and the issue was resolved in the next version).
The messages would multiply as well. First, there were only two messages. Then 6 or 7. Then 12. Currently the number is at 20. As far as I know, there is no way to remove them.
I may have discovered that this bug is related to another bug I found and thought others would report on, as when I accidentally reproduced the issue described below, it seemed new Blank IdReference messages were made. Whenever I copy a frame from one sprite to another in the sprite editor and the number of layers from the copied sprite is higher than those on the sprite the frame is pasted on to, the new frame creates new layers, as is expected. But what isn't expected is that all of the layers are called Default, and, unless you exit and reopen the project or the layers have no drawn pixels of what I believe to be any alpha greater than zero, the layers that are created on paste will be identified as a error frame, despite initially seeming perfectly replicated. drawing on the frame only snaps the frame back to the state before it was drawn, as if someone had pressed the undo button. Hiding the layers and then showing them again reveals a variety of behaviors ranging from showing hidden layers to showing an error image to seeming normal but not being able to edit on the layers. As said before, a simple reopening of the project fixes this issue. Even then, it's still up in the air whether or not the pasted frames will have the intended images. All of these behaviors occur independent of any difference in the size of the Sprites.
I'm currently unable to prove whether or not my theory that the two bugs are related is true. After reproducing the phantom layers bug for this post, the Blank IdReferences did not increase.
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