Yes, you can choose to reload only some of your datasets while keeping others intact.

Another option is to use the "Query Snapshot" feature of study queries to create a study dataset from an external schema.

You would create a new query in your study schema that selects the desired columns from your source schema. E.g. given an external schema "mark" I could create a query in the study schema like so:

select ptid as participantid, sequencenum, date from mark.ptidtest

You could then use Views->Create->Query Snapshot to create a dataset from the results of the query. You can choose whether you want that dataset updated automatically (every n minutes) or manually.