Fix bgupdate error if index already exists (#2167)
When creating a new table index in the background, guard against it existing already. Fixes https://github.com/matrix-org/synapse/issues/2135. Also, make sure we restore the autocommit flag when we're done, otherwise we get more failures from other operations later on. Fixes https://github.com/matrix-org/synapse/issues/1890 (hopefully).
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