It is not possible to tell Thinking Sphinx to process one index at a time, but it is certainly possible (and not particularly difficult) using the Sphinx index index tool directly.
indexer --config config/development.sphinx.conf model_core
A few notes: if you do not specify the proper names for the index definitions, the model name will be specified by default, reduced and underlined with the suffix _core. If you had delta indices in the game, they would have the _delta suffix. Also, add the --rotate flag to this call if Sphinx is running.
You can specify as many indexes as you want. If you ever want to process all indexes at once (just like Thake Sphinx rake task), --all will do it for you.
As an aside - how many records are we talking about? How complicated are your index definitions? Several hours of processing indexes are not ordinary. Do you have database indexes for any foreign key columns used by associations specified in Sphinx indexes?
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