Quote from Superjager
if you try to dig with a tool that has the flux upgrade while a TE3 flux capasitor charges you tool you can't dig any blocks until it if full
hope it helps
Every time the item you're holding changes (A pick with more charge is not the same pick as before), the game makes you reset any length of progress that you've mined on a block. This was changed at some point, to prevent switching picks to save on durability.