Hey, I'm using version 3.4.9 and I'm having a similar issue trying to update the atlas. I'm trying to make an equipment inventory atlas and I keep getting an error saying:
"MissingReference Exception: The object of type 'Texture2D' has been destroyed but you are still trying to access it"
after trying to update. The atlas maker also never finished updating the atlas. It gets to the end of the loading bar, and stops so I can click Add/Update again. Once or twice, clicking the update button again will add the image to the atlas, but more often than not it will restart the update bar and never finish the update.
When it works fine, it moves onto a "Hold On" Loading bar, and adds the image from it's destination folder.
I've read through many of the atlas maker posts and have found nothing that consistantly works. I've tried waiting for longer times, clicking add/update multiple times, and adding the short line of script to the UI Atlas Maker script:
"sprite.tex.hideFlags = HideFlags.HideAndDontSave;"
as posted by Muxeu but it's made no difference. I've also tried it on different computers and it makes no change. Any assistance would be appreciated.