I have had a chance to write the code, but am some how fundamentally misunderstanding something or have made a daft error I cannot see. The following code runs through, but no changes to the metadata are checked in to the workspace, stepped through the code and the right things are being extracted and passed to the set user properties code and nothing gives me an error, probably need to connect to something or disconnect to something to concrete the change. Anyway here is the relevant code, can someone tell me what is wrong with it. Note I am using global variables and a recursive procedure, then applying all the changes to the workspace at the same time using the save operations "ops" global variable filled out in the recursive procedure. Any pointers appreciated probably some daft mistake.

Note I expect my error is in this bit of code: -

v.setUserProperty(metaDataFieldsToExtract[i], metaDataStr);
// Save the change into a change set  
ISaveOp saveOp = opFactory.save(file);
ops.add(saveOp);

Here comes the code listing : -

 List<IWorkspaceHandle> workspaces = findConnectionByName(teamRepository,tempWorkSpace, IWorkspaceSearchCriteria.WORKSPACES, monitor);
 IWorkspaceHandle firstFound = null;
 IWorkspaceConnection connection = null;
 if (!workspaces.isEmpty()) {
  firstFound = workspaces.get(0);
  connection = wm.getWorkspaceConnection(firstFound, monitor);
 }
        //If we find our workspace then we need to get our component from it - but component can be in many workspaces, but only one owner
        //things could go horribly wrong here, can't easily search for components on workspace
        //MAKING SWEEPING ASSUMPTION DANGER OF BITING ME IN ASS!
        if(connection != null) {
            IComponentHandle mycomp;
            IComponentSearchCriteria fred = IComponentSearchCriteria.FACTORY.newInstance();
            fred.setExactName(componentAndEcProjName);

            List<IComponentHandle> comps = wm.findComponents(fred, 20, monitor);

            mycomp = comps.get(0);

            if(myTeamArea != null) {
                wm.setComponentOwnerAndVisibility(mycomp, myTeamArea, IReadScope.FACTORY.createTeamAreaPrivateScope(), monitor);
            }
            else {
                wm.setComponentOwnerAndVisibility(mycomp, projectArea, IReadScope.FACTORY.createProcessAreaScope(), monitor);
            }

            IConfiguration compConfig = connection.configuration(mycomp);
            IFileContentManager contentManager = FileSystemCore.getContentManager(teamRepository);
            IConfigurationOpFactory opFactory = connection.configurationOpFactory();
            ops = new ArrayList<IWorkspaceConnection.IConfigurationOp>();

            // Fetch the items at the root of each component. We do this to initialize our
            // queue of stuff to download.
            Map<String, IVersionableHandle> handles = compConfig.childEntriesForRoot(null);
            List<IVersionable> items = compConfig.fetchCompleteItems(new ArrayList<IVersionableHandle>(handles.values()), null);
            //Need to get childEntries from handles map too as does not seem to recurse down, may need recursive procedure - bit of a pain!!                  
            getMetaDataRecurse(contentManager, compConfig, rootFolder + "/", items, opFactory);

            // create a change set for our metadata changes
            IComponent richardsComponent = findComponent(teamRepository, connection, componentAndEcProjName);
            IChangeSetHandle cs = getOrCreateChangeSetInComponent(connection,richardsComponent);
            System.out.println("Committing meta data to workspace");
            connection.commit(cs, ops, null);
            connection.closeChangeSets(Collections.singletonList(cs), null);
            SCMPlatform.getWorkspaceManager(teamRepository).setComment(cs, "Added Dimensions metadata", null);
        }
 
 private static void getMetaDataRecurse(IFileContentManager contentManager, IConfiguration compConfig, String path,
   List<IVersionable> toLoad, IConfigurationOpFactory opFactory)
   throws FileNotFoundException, TeamRepositoryException, IOException {
          String[] metaDataFieldsToExtract = {"file-version", "item-status", "project", "item-spec", "item-uid", "project-uid"};
                Pattern[] MetaFieldPatterns = new Pattern[metaDataFieldsToExtract.length];
                for(int i=0;i<metaDataFieldsToExtract.length;i++ ) {
                     MetaFieldPatterns[i] = Pattern.compile("^" + metaDataFieldsToExtract[i] + "=(.*)",Pattern.MULTILINE );
                }

  for (IVersionable v : toLoad) {
   if (v == null) {
    // The versionable will be null if we don't have permission to read it
    continue;
   }
   
   if (v instanceof IFolder) {
    // Write the directory
    String dirPath = path + v.getName() + "/";
    
    
    @SuppressWarnings("unchecked")
    Map<String, IVersionableHandle> children = compConfig.childEntries((IFolderHandle)v, null);
    @SuppressWarnings("unchecked")
    List<IVersionable> completeChildren = compConfig.fetchCompleteItems(new ArrayList<IVersionableHandle>(children.values()), null);

    getMetaDataRecurse(contentManager, compConfig, dirPath, completeChildren, opFactory);
   }
   else if (v instanceof IFileItem) {
    // Get the file contents and write them into the directory
    IFileItem file = (IFileItem) v;
                                file = (IFileItem) file.getWorkingCopy();

                                //need to grab metadata at this point can do this by getting the name then runniing dmmetadata then adding properties from here                                                           
                                String FullFile= path + v.getName();
                                
                                System.out.println(FullFile);
                                String dmMetaCommand =  dimensionsLocation + "\\dmmeta.exe get \"" + FullFile + "\" --file c:\\temp\\output.txt";
                                execConsoleCommand(dmMetaCommand);
                                FileInputStream readTempFile = new FileInputStream(new File("c:\\temp\\output.txt"));
                                String metaDataFieldsToProcess = IOUtils.toString(readTempFile);

                                for(int i=0;i<metaDataFieldsToExtract.length;i++ ) {
                                    Matcher findMetaDataHex = MetaFieldPatterns[i].matcher(metaDataFieldsToProcess);
                                    if(findMetaDataHex.find()) {

                                        String metaDataStr = findMetaDataHex.group(1).toString();
                                        if(Pattern.matches("^[A-F0-9]+$", metaDataStr) && metaDataStr.length() % 2==0 && metaDataStr.length()>4) {
                                             metaDataStr = hexToASCII(metaDataStr);
                                        }

                                      v.setUserProperty(metaDataFieldsToExtract[i], metaDataStr);
                                    }
                               }
                                // Save the change into a change set  
                                ISaveOp saveOp = opFactory.save(file);
                                ops.add(saveOp);

   }
   else {
    // The item could be a symlink or an even more exotic type of versionable. Skip it. 
    System.err.println("Cannot load " + v.getName() + " of type " + v.getClass().getSimpleName());
   }
  }
 } 

Might have got my versionables and fileworkingcopies mixed up!

works a lot better when you change

v.setUserProperty

to

file.setUserProperty