You need to tell the environment to ignore file changes. This can be achieved using the IVsFileChangeEx and IVsDocDataFileChangeControl interfaces.

Here is a utility class (derived from the original Visual Studio 2010 SDK Managed Package Framework sample that you can still find here: http://www.getcodesamples.com/src/8641B4F/98B3955E) that should help:

using (SuspendFileChanges suspend = new SuspendFileChanges(site, filePath))
{
    // do something with files
    suspend.Sync(); // if you optionally want to tell the IDE it has changed
}

The utility class:

public class SuspendFileChanges: IDisposable
{
    private readonly IServiceProvider _serviceProvider;
    private readonly List<string> _urls;
    private readonly IVsDocDataFileChangeControl[] _controls;

    public SuspendFileChanges(IServiceProvider serviceProvider, string url)
        : this(serviceProvider, new string[] { url })
    {
    }

    public SuspendFileChanges(IServiceProvider serviceProvider, params string[] urls)
    {
        if (serviceProvider == null)
            throw new ArgumentNullException("serviceProvider");

        if (urls == null)
            throw new ArgumentNullException("urls");

        _serviceProvider = serviceProvider;
        _urls = new List<string>(urls);
        _controls = new IVsDocDataFileChangeControl[_urls.Count];

        // or use Package.GetGlobalService ...
        IVsRunningDocumentTable rdt = (IVsRunningDocumentTable)serviceProvider.GetService(typeof(SVsRunningDocumentTable));
        IVsFileChangeEx fileChange = (IVsFileChangeEx)serviceProvider.GetService(typeof(SVsFileChangeEx));

        for(int i = 0; i < _urls.Count; i++)
        {
            string url = _urls[i];
            if (url == null)
                continue;

            fileChange.IgnoreFile(0, url, 1);

            IVsHierarchy hierarchy;
            uint itemId;
            uint docCookie;
            IntPtr docData;
            rdt.FindAndLockDocument((uint)_VSRDTFLAGS.RDT_NoLock, url, out hierarchy, out itemId, out docData, out docCookie);
            if (docData != IntPtr.Zero)
            {
                _controls[i] = Marshal.GetObjectForIUnknown(docData) as IVsDocDataFileChangeControl;
                if (_controls[i] != null)
                {
                    _controls[i].IgnoreFileChanges(1);
                }
                Marshal.Release(docData);
            }
        }
    }

    public void Sync()
    {
        IVsFileChangeEx fileChange = (IVsFileChangeEx)_serviceProvider.GetService(typeof(SVsFileChangeEx));
        if (fileChange == null)
            throw new InvalidOperationException();

        foreach (string url in _urls)
        {
            if (url == null)
                continue;

            fileChange.SyncFile(url);
        }
    }

    public void Dispose()
    {
        IVsFileChangeEx fileChange = (IVsFileChangeEx)_serviceProvider.GetService(typeof(SVsFileChangeEx));
        if (fileChange != null)
        {
            foreach (string url in _urls)
            {
                if (url == null)
                    continue;

                fileChange.IgnoreFile(0, url, 0);
            }
        }

        foreach (IVsDocDataFileChangeControl control in _controls)
        {
            if (control != null)
            {
                control.IgnoreFileChanges(0);
            }
        }
    }
}