I need to free some disk space in bitcoin server.
Will bitcoind download all blocks from scratch again if I change 'prune' value in bitcoin.conf over working daemon?
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The prune value merely sets the limit of how much block data is kept.
If you increase the value and restart, no block data will be deleted for a while. New blocks will be received and validated and stored, and old ones won't be deleted until the new prune value is reached again.
If you decrease the value and restart, the oldest blocks will be deleted at startup.
You cannot go from pruned to nonpruned. That requires starting over.