That will normally work as long as you do it using the Package Explorer, and you allow Eclipse to "update references." I think that's what it's called. Eclipse gives you the option to skip that step, and if you do, you're likely to end up with a confused workspace that you'll have to clean up manually. That's what you just did, and it wasn't that big of a deal.
Also, the "Run" button and corresponding run list will become confused at times. When selected, the run button attempts to run the currently selected class, but if the currently selected class doesn't contain a main() method, it will run the last class run at the top of the run list. If the workspace becomes muddled, the run list may not be correct anymore, containing a class that no longer exists or whose name has changed, etc. Running the desired class may require right clicking the class and selecting Run As as you did earlier.
The good news is that you have to work incredibly hard to confuse Eclipse so badly that source files are lost.