If you have a compressor failure, it's a great idea to flush the AC system out before installing your new one. Many times when a compressor fails it sends small metal particles throughout the AC system. These particles clog up the small passages in the system and cause problems after you've replaced the failed compressor. In fact, you run the risk of damaging your new compressor with these small metal particles. For that reason you should always flush the AC system with a special cleaner whenever you replace a failed compressor. It's also a good idea to replace the orifice tube or screen when you have a compressor failure. Some new compressors come with these parts in a kit.
In summary, anytime you have an AC system that's been contaminated, you should flush it out before putting it back into service.