To start, please take a look onto [https://netbeans.org/bugzilla/show_bug.cgi?id=65135#c40] to get idea of how expensive File.isFile() is.

Next, lets look onto this code:
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    private List<Coordinates> getJarMetadataCoordinatesIntern(File binaryFile) {        
        if (binaryFile == null || !binaryFile.exists() || !binaryFile.isFile()) {
            return null;
        }        
        synchronized (coorCache) {
            List<Coordinates> toRet = coorCache.get(binaryFile);
            if(toRet == null) {
                toRet = getJarMetadataCoordinates(binaryFile);         
                if(toRet != null) {
                    FileUtil.addFileChangeListener(binaryChangeListener, binaryFile);
                    coorCache.put(binaryFile, toRet);
                }                
            } 
            return toRet;
        }
    }
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Double-check for existence of file is already mentioned in #65135. Another issue is - expensive binaryFile.isFile() can be avoided at all by moving that verification under 'if(toRet == null)' - when that file is actually going to be used. 

'Removal' of the file should be traced by attached fileChangeListener - therefore verification for existence is not needed while file is in cache (i guess).

On more issue here - code forwarded to "toRet = getJarMetadataCoordinates(binaryFile);" performs double check for file existence once again. I would refactor code like following:

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    private List<Coordinates> getJarMetadataCoordinatesIntern(File binaryFile) {        
        if (binaryFile == null ) {
            return null;
        }

        synchronized (coorCache) {
            List<Coordinates> toRet = coorCache.get(binaryFile);
            if(toRet == null) {
                if( !binaryFile.isFile() )
                    return null;
                
                toRet = getJarMetadataCoordinates(binaryFile, false);         
                if(toRet != null) {
                    FileUtil.addFileChangeListener(binaryChangeListener, binaryFile);
                    coorCache.put(binaryFile, toRet);
                }                
            } 
            return toRet;
        }
    }
    
    public static List<Coordinates> getJarMetadataCoordinates(File binaryFile) {
        return getJarMetadataCoordinates(binaryFile, true);
    }
        
    public static List<Coordinates> getJarMetadataCoordinates(File binaryFile, boolean checkExists) {
        if (binaryFile == null || checkExists && !binaryFile.isFile()) {
            return null;
        }        

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That change brings negative effect of that issue [https://netbeans.org/bugzilla/show_bug.cgi?id=268028] close to zero.