There's nothing in Thinking Sphinx for customising the offset for document ids, nor selectively overwriting the configuration file. It's pretty much all-or-nothing at this point.
So, I'd recommend you use rake ts:reindex, which only indexes, and doesn't overwrite the configuration file. And if you want to patch to allow for custom offsets, I'd definitely be interested in seeing your approach. And am especially looking forward to your writeup of how you manage a distributed search setup.
Cheers
--
Pat
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