You will be okay if you just pour in some mineral oil and turn the shaft by hand some to circulate it through and then pump and pour out as much as you can get. You are right, DON'T use any flushing agent in the compressor.

I'm assuming you are flushing the entire system. Make certain that you get ALL of the flushing agent out of the system. After that put a few ounces of oil in several places as you put things back together to distribute a total of 6 ounces of Mineral oil throughout the system.

If you're not flushing the entire system, and since it has always been R12 and the compressor didn't scatter, you shouldn't really need to, Just put a few ounces of mineral oil in the compressor. Mineral oil will work great in an R12 system. There are some folks who will want to sell you a magic oil, but mineral oil will work great.

Put on the filter drier last after everything else is in place and sealed up. This will minimize the contamination of the new r/d. Pump it down a long time since the system has been opened.

Good lu