It is a valid way of doing things but you could also consider keeping the files separate and using different strategies to make compiled files. If you are having problems only when you merge docs then it can be easier to just keep them separate. If keeping separate you have few options:
1. Using RD fields to build TOCs and/or Indexes. Output docs to a combined PDF version for current versions.
2. Use includetext fields to import the current versions of the parts into a single doc
3. Use Master Docs feature and be careful to ONLY edit the separate chapters as standalone docs.

Options 2 and 3 might require you to structure your multi-level list styles a particular way so the merger doesn't make separate lists continue numbering. I would need to see your docs to give more detailed guidance on managing the lists so they work correctly in standalone and merged modes.

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Andrew Lockton
Chrysalis Design, Melbourne Australia