1. Tom had done the work for two hours when I called him.
2. Tom had been doing the work for two hours when I called him.
Are the above sentences acceptable?
I would opt for "had been doing". He started the work two hours before I called him and was still doing it when I called. Past perfect continuous goes well with duration.
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I would opt for "had been doing". He started the work two hours before I called him and was still doing it when I called. Past perfect continuous goes well with duration.
"Had done" expresses completion, the work was done, finished.
In addition to what has been said, note that the verb work is, in my experience, more common than do the work.
1. Tom had worked for two hours when I called him.
2. Tom had been working for two hours when I called him.