Not much experience directly with Aldon, but from my experience with change control systems, if you change the file (table or PF) the index is built over and you don't have source for the index in the source control system it can't be rebuilt over the new version of the file as part of the change.
I would expect you would get an error of some kind to inform you that your losing the index.
Follow the directions of the previous responders and get source for the index and incorporate it into the change process.

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