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There is a difference between short term RV and long term RV. It is of course not useful to take a short term RV position with a relative value of 5bps if it will have a range of 4-6bps in the foreseeable future, but in the long term it is likely to be positive.
The effects you mention are valid reasons why bonds from the same issuer cannot be fully priced ...
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You could decompose the portfolio dv01 by buckets (corresponding to the available futures) and hedge each bucket with the appropriate number of contracts.
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