Skip file when entering some Exception

Your method is crashing because your try / catch is out of order and when an exception is thrown, the loop is broken. You simply move the try / catch into the for and it will try to read all the files.

In order for it to try to read the files that fail again, you can store them in a list and then try to read them again. It would look something like this:

public static String lerPasta() {

    FileFilter filter = new FileFilter() {
        public boolean accept(File file) {
            return file.getName().endsWith(".pdf");
        }
    };

    File dir = new File(FILE_PATH);
    Iterator<File> files = Arrays.asList(dir.listFiles(filter)).iterator(); 
    List<File> failedFiles = new ArrayList<>();

    while(files.hasNext()) {
        File file = files.next();
        try(Scanner s = new Scanner(new File(file.toString()), "UTF-8")) {
            //Faça o que quiser aqui
            //...
        } catch (FileNotFoundException | NoSuchElementException e) {
            if(failedFiles != null) {
                failedFiles.add(file);
            }
        } finally {
            if(!files.hasNext() && failedFiles != null && !failedFiles.isEmpty()) {
                files = failedFiles.iterator();
                failedFiles = null;
            }
        }
    }

}

It will crash because the for is inside the try-catch, as soon as the exception is thrown ( FileNotFoundException or NoSuchElementException ), it will exit the for and enter the catch.

Try to do that. I took it out from inside the catch, and put another one inside it (from for). This try-catch inside for will ignore the "faulty" files.

Just to remember, it's not cool to be using pure try-catch, that is, hiding exception, the reason has to be very good.

public static String lerPasta() throws FileNotFoundException{
      String texto = null; 
      File[] files = null;    
        try{    
            FileFilter filter = new FileFilter() {
            public boolean accept(File file) {
                return file.getName().endsWith(".XML");
                }
            };
            File dir = new File(diretorioIn);
               File[] files = dir.listFiles(filter);

        }catch(FileNotFoundException e){
                 System.out.println(ZonedDateTime.now(fusoHorarioDeSaoPaulo)+"lerPasta():ERRO: FileNotFoundException : Tentando novamente ...");
        }    
        catch(NoSuchElementException e){
             System.out.println(ZonedDateTime.now(fusoHorarioDeSaoPaulo)+"lerPasta():ERRO: NoSuchElementException : Tentando novamente ...");
        }

        if(files == null){
            //Lança algum erro.
        }

        for(i = 0; i < files.length ; i++){
            try{
                Scanner s = new Scanner(new File(files[i].toString()), "UTF-8");
                texto = s.useDelimiter("\A").next();     
                System.out.println(ZonedDateTime.now(fusoHorarioDeSaoPaulo)+"VALOR DE I" +i);
                verificaTipoXML(files[i].toString().substring(diretorioIn.length()));
                System.out.println(ZonedDateTime.now(fusoHorarioDeSaoPaulo)+" verificaTipoXML:files[i].toString(): "+files[i].toString());
                System.out.println(ZonedDateTime.now(fusoHorarioDeSaoPaulo)+" lerPasta():" + files[i].toString());
                System.out.println(ZonedDateTime.now(fusoHorarioDeSaoPaulo)+" verificaTipoXML():" + files[i].toString().substring(diretorioIn.length()+0));
                deleta = files[i].toString();
                //+1
                deleta2 = files[i].toString().substring(diretorioIn.length());
                deletar = files[i];
                System.out.println(ZonedDateTime.now(fusoHorarioDeSaoPaulo)+" deleta:"+deleta2);
                nomegerado = files[i].toString().substring(diretorioIn.length()+3);
                System.out.println(ZonedDateTime.now(fusoHorarioDeSaoPaulo)+" GLOBAL:nomegerado:" + nomegerado);
            }catch(AlgumaException e){
                //Não faz nada.
            }finally{
                s.close();
            }
        }
    return texto;
}