Hello! Looking at this now, it seems that spawners vanishing like this could be a result of a wide variety of different things (item naturally despawning after 5 minutes, the item falling off the island, someone else picking up the item, etc.). I've put in some fixes specifically with ore generators when it comes to removing them where sometimes the ore generator would be launched off the map.
My suggestion going forward would be to keep some inventory slots open when breaking spawners just so there is less of a chance of them despawning or any of the above from happening. If you notice something completely out of the ordinary happen, such as the spawner item vanishing right in front of you, please open a bug report (if you have video evidence, please provide it as well).