try making the calulation unstored, and get the fields from the other files directly, not through look-ups. (Use the actual field in the calculation rather than a lookup field.)
MikeyG79's suggestion will certainly solve the automatic update issue, but sometimes you need the value to be a stored value as it might be a key field or a field used in find/sort operations.
If you have to, you can script a relookup of looked up values. There's a script step with exactly that name you can use. In FMP 10 you can set this up with a script trigger. The practicality of this approach and the details of how you would implement it depend on your database design and the sheer number of records that need the update each time a field is changed.