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I had a biochamber producing bioflux and at some point processing was halted long enough for the input items to spoil. even though I had an assembler set to remove spoilage, this does not seem to clear stuff from the input slots. am I missing something or is this a manual cleanup task?

Probably your output was full?

Then it looks like that (inserters won't pick it up): Now inserters pick it up: The spoiled items are getting moved automatically to the output slot, when it becomes free. No manual action required.

cool, thanks