Yes, these oils are termed "Universal Grade". I don't know where that comes from, I suppose because they can be used for diesel and gas engines.
I don't know what oil you used previously, but it should have a "C" classification, such as CF or CH. I doubt that you did damage, and I wouldn't worry about flushing it. The best way to "flush" it would be to pull the drain plug after the engine has reached operating temperature(at least 17 miles of driving) and let it drain overnight.
I have used Chevron Delo 400 Multigrade, but Shell Rotella, Mobil Delvac are all good diesel engine oils. If you really want to give your engine a good diet, put it on the new Mobil Delvac One, which is Mobil One synthetic in universal grade for diesels. I doubt that it is inexpensive, and you will probably have to find a truck stop to get it. If you're interested, you can probably call your local Cummins or International dealer to find it.
Change oil hot, and change oil often,
'01 C Class, Six Speed
'84 Euro 240D, manual, 533K miles
'88 300E 5 Speed
'81 300D Daughter's Car
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