I've seen this too occasionally, seems to be a bug in Flash Builder. Even a full Refresh / Clean & Build All doesn't always fix it. Have to exit, restart Flash Builder and do another Clean & Build All.
Even with a clean and I can see the files being replaced it still is not running the updated files for some weird reason.
I had a similar problem, for which I post the link below, but I never found a solution, so please don't expect too much insight from reading the discussion.
I occasionally run into this as well. Very frustrating.
Is the SWF hosted on a web server? It may be getting cached by the browser.
Can you post your Flash Builder log the minute after you run into this problem the next time? The log is at workspacedir/.metadata/.log
Usually when Flash Builder performs an incremental compilation and something goes wrong, "An internal build error occurred" will appear in the Problems view.
I seemed to have figured this out.
1) You must have 0 errors in the problems log when compiling
2) You may need to press the refresh button on your browser
3) If that doesn't work you can clean out your temp internet files.
The problem for me seemed to be that I needed to refresh the page. Not sure why. I hope this helps someone else too!
I've recently been experiencing an abnormal number of occurrences of this error and Google directed me to this thread. In response to your question, here's the Error Log message that gets added when the "internal build error" occurs:
Mon Aug 06 13:11:03 EDT 2012
Uncaught exception in compiler
at com.adobe.flexbuilder.project.ui.utils.ANE.AppXMLFileANEExtensionHandler.addToAppXmlFile( AppXMLFileANEExtensionHandler.java:74)
at com.adobe.flexbuilder.project.ui.utils.ANE.AppXMLFileANEExtensionHandler.addToAppXmlFile( AppXMLFileANEExtensionHandler.java:46)
at com.adobe.flexbuilder.project.ui.utils.ANE.ANEController.applyWorkingCopy(ANEController.j ava:720)
at com.adobe.flexbuilder.project.ui.utils.ANE.ANEController.projectIsBuilt(ANEController.jav a:904)
at com.adobe.flexbuilder.project.compiler.internal.FlexProjectBuilder.informProjectBuildList ener(FlexProjectBuilder.java:156)
at com.adobe.flexbuilder.project.compiler.internal.FlexProjectBuilder.buildItem(FlexProjectB uilder.java:616)
at com.adobe.flexbuilder.project.compiler.internal.FlexProjectBuilder.build(FlexProjectBuild er.java:382)
at com.adobe.flexbuilder.project.compiler.internal.FlexIncrementalBuilder.build(FlexIncremen talBuilder.java:187)
My particular project is a Flex Mobile project with a couple of ANEs. I have to restart Flash Builder every couple of times I launch my project though because of this type of error.
Any ideas? Could I provide you with any more information to help track down the problem?
I am experiencing the same exact error as Brian above. Does anyone have any clues as to what's wrong here? It's only happening when I try to compile an AIR application for mobile development, and I'm running FB 4.6. I've tried using different versions of the Flex/AIR SDK to no avail.