I have added confirmation dialog to inform user that file will be replaced.
But making file path field editable is considered as topic for another issue.

fixed in main trunk
http://hg.netbeans.org/main/rev/f2aba681c5bc

ask user to confirm rewriting. 
delete existing file before creating new with the same name.

changing TM to the right one

Reopening - reproduced in NetBeans IDE 6.5 (Build 200811100001)
http://statistics.netbeans.org/exceptions/detail.do?id=42983

Build: NetBeans IDE 6.5 (Build 200811100001)
VM: Java HotSpot(TM) Client VM, 11.0-b15, Java(TM) SE Runtime Environment, 1.6.0_10-b33
OS: Windows XP, 5.1, x86

User Comments: 
I renamed a project.

Stacktrace: 
java.io.SyncFailedException: D:\Users\Documents\Java projects\WetCom\x\DesktopAppTestModule2\nbproject\private\config.properties
        at org.netbeans.modules.masterfs.filebasedfs.fileobjects.FolderObj.createData(FolderObj.java:287)
        at org.netbeans.modules.masterfs.filebasedfs.fileobjects.FolderObj.createDataImpl(FolderObj.java:245)
        at org.netbeans.modules.masterfs.filebasedfs.fileobjects.FolderObj$1.call(FolderObj.java:215)
        at org.netbeans.modules.masterfs.filebasedfs.fileobjects.FolderObj$1.call(FolderObj.java:214)
        at org.netbeans.modules.masterfs.filebasedfs.FileBasedFileSystem.runAsInconsistent(FileBasedFileSystem.java:112)
        at org.netbeans.modules.masterfs.filebasedfs.fileobjects.FolderObj.createData(FolderObj.java:218)

Created attachment 76443 [details]
stacktrace

first filed exception is in mobility but is fixed.
Exception that caused issue reopening is from j2se projects.

Therefore reassigning issue to java. 
I'm also changing a summary.

I am wondering if this issue occurs either immediately preceding the project being re-shown in Projects, or sometime 
just afterward. In my case, I refactor/renamed a Java class library (out of 4 opened classlib projects) which was 
previously selected as the main project, but after the rename, this library project was not bolded indicating it was 
still set as the main project.
Probably related to the project being removed from the projects view, then re-added without concern for if it was 
previously a main project....
I hope this perspective is useful in diagnosing the problem.

I am not able to reproduce this bug on current trunk version. I am trying different combinations of project create /
rename / configuration create / change / set main project / open and close project, and everything works. I am not able
to fix it without reproducible usecase. Can somebody attach some steps, please?

with almost all of these exceptions, they aren't really what the description says. yes, the stack trace is the visible
manifestation, but the real problem happened before the stack trace. some sort of cache or index corruption. once that
happens, almost any refactoring or searching action will cause exceptions

don't expect reproducibility, and don't think that because you can't reproduce it that it doesn't exist

Resolving all issues with milestone "future" as LATER. If you feel strongly that
it should be implemented please reopen and set the target milestone to "next".

(I'm reopening this issue as I'm not quite sure whether you'll get an email if it is closed.
Please close it again if ther is not enough information to fix it.)

Just found this issue while investigating another bug.
The corresponding piece of code in my module:

        FileObject gwt = libsFolder.getFileObject(libxml);
        if (gwt == null) {
            gwt = libsFolder.createData(libxml);
        }

So clearly the file does *not* exist as it is created.

and the exception is:

SEVERE: File gwt1.6.4.xml already exists in filesystem 
/Users/jean/.netbeans/6.7/config (/Users/jean/.netbeans/6.7/config/org-
netbeans-api-project-libraries/Libraries/gwt1.6.4.xml).
msg
Caused: java.io.SyncFailedException: File gwt1.6.4.xml already exists in 
filesystem /Users/jean/.netbeans/6.7/config 
(/Users/jean/.netbeans/6.7/config/org-netbeans-api-project-
libraries/Libraries/gwt1.6.4.xml).
        at 
org.openide.filesystems.LocalFileSystem.createData(LocalFileSystem.java:278)
        at 
org.openide.filesystems.LocalFileSystem$Impl.createData(LocalFileSystem.java
:555)
        at 
org.openide.filesystems.AbstractFileObject.createData(AbstractFileObject.java
:470)
        at org.openide.filesystems.FileUtil.createData(FileUtil.java:798)
        at 
org.openide.filesystems.MultiFileObject.createData(MultiFileObject.java:1085)
        at org.openide.filesystems.FileUtil.createData(FileUtil.java:798)
        at 
org.openide.filesystems.MultiFileObject.createData(MultiFileObject.java:1085)
        at org.openide.filesystems.FileObject.createData(FileObject.java:820)
        at 
org.netbeans.modules.gwt4nb.GWTFrameworkProvider.createGWTUserLibrary
(GWTFrameworkProvider.java:549)
        at 
org.netbeans.modules.gwt4nb.GWTFrameworkProvider$1.run(GWTFramework
Provider.java:114)
        at 
org.openide.filesystems.EventControl.runAtomicAction(EventControl.java:120)
        at 
org.openide.filesystems.FileSystem.runAtomicAction(FileSystem.java:509)
[catch] at 
org.netbeans.modules.gwt4nb.GWTFrameworkProvider.extend(GWTFramewor
kProvider.java:98)
        at 
org.netbeans.modules.web.webmodule.WebModuleExtenderBridge.extend(We
bModuleExtenderBridge.java:111)
        at 
org.netbeans.modules.web.project.ui.wizards.NewWebProjectWizardIterator.in
stantiate(NewWebProjectWizardIterator.java:184)
        at 
org.openide.loaders.TemplateWizard$InstantiatingIteratorBridge.instantiate(T
emplateWizard.java:1016)
        at 
org.openide.loaders.TemplateWizard.handleInstantiate(TemplateWizard.java:5
88)
        at 
org.openide.loaders.TemplateWizard.instantiateNewObjects(TemplateWizard.j
ava:409)
        at 
org.openide.loaders.TemplateWizardIterImpl.instantiate(TemplateWizardIterI
mpl.java:253)
        at 
org.openide.loaders.TemplateWizardIteratorWrapper.instantiate(TemplateWiz
ardIteratorWrapper.java:165)
        at 
org.openide.WizardDescriptor.callInstantiateOpen(WizardDescriptor.java:1524
)
        at 
org.openide.WizardDescriptor.callInstantiate(WizardDescriptor.java:1481)
        at 
org.openide.WizardDescriptor.access$1700(WizardDescriptor.java:127)
        at 
org.openide.WizardDescriptor$Listener$2$1.run(WizardDescriptor.java:2052)
        at 
org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:577)
        at 
org.openide.util.RequestProcessor$Processor.run(RequestProcessor.java:1030
)
ALL [null]: File gwt1.6.4.xml already exists in filesystem 
/Users/jean/.netbeans/6.7/config (/Users/jean/.netbeans/6.7/config/org-
netbeans-api-project-libraries/Libraries/gwt1.6.4.xml).
INFO [org.netbeans.modules.parsing.impl.indexing.RepositoryUpdater]: 
Resolving dependencies took: 10 ms

stacktrace was added. Could you please re-evaluate? Thanks.

To lebedkov: It's safer to use FileUtil.createData(File) than the FileObject.createData() in such a case.

Fixed in jet-main dc8aae6de684

Integrated into 'main-golden', will be available in build *200910030241* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress)
Changeset: http://hg.netbeans.org/main-golden/rev/dc8aae6de684
User: Tomas Zezula <tzezula@netbeans.org>
Log: #131943:java.io.SyncFailedException when renaming a project

Integrated into 'main-golden', will be available in build *200910061401* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress)
Changeset: http://hg.netbeans.org/main-golden/rev/dc8aae6de684
User: Tomas Zezula <tzezula@netbeans.org>
Log: #131943:java.io.SyncFailedException when renaming a project