When cobblestone has been smelted into regular stone and then moved into a chest via hopper, that stone cannot be smelted again to make smooth stone and will also refuse to stack with stone not smelted from the hopper-furnace
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We're tracking this issue in MCPE-47907, so this ticket is being resolved and linked as a duplicate.
That ticket has already been resolved as Fixed. The fix will arrive in the next version or is already included in the latest development version of the game, you can check the Fix Version/s field in that ticket to learn more.
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Bump... can't smelt smooth stone unless it's been mined with silk touch