The bpel-deploy.xml file is actually saved, however appears to not be saved by 2 visual indicators: the Save icon in the tool bar and the file name *bpel-deploy.xml in the Tab
1) Click File / New / Other
2) Select Apache ODE Deployment Descriptor
3) Click Finish
4) Change something in the Deployment descriptor, such as checking/unchecking "Run this process in memory"
5) The Save icon on the toolbar is now enabled
6) Click the Save icon in the toolbar
7) The Save button in the toolbar is still enabled and in the Tab with the file name "bpel-deploy.xml" still shows "*bpel-deploy.xml", which makes it look like the file has not been saved even though it has.