If you did a reinstall or a -clean, it is *possible* that the setting to SHOW those warnings was turned back on (Window > Prefs > Java > Debug > “Show error when hotcode replace fails”)
Regardless, this is an Eclipse debugger setting, MyEclipse doesn’t effect it, so I’m guessing it just got turned on. I checked mine and it is turned off and I usually run with default settings.
Also note that in my experience, even though you get that message, the app will likely keep working just fine as Tomcat will usually reload the file without problems. However if the app server eventually dies with a VM termination, just restart it. Usually it gets overwhelmed with too many complex hotcode replacements. I like to just turn that warning off and keep working and just wait to see the console messages from Tomcat when it reloads my file before trying the page again that uses the code.