Converting fat to muscle (by eating well, doing training and including the right amount of rest) is usually helpful.
Converting fat to the sorts of muscles you are going to use to run (by eating what best suits you and your goals, run-specific training and including the right amount of rest) is even better.
If you lose some weight while doing so, and (as several people before me have already stated) you remain heavy enough to maintain your long-term health, that's a bonus.