Thank you for contacting us with this.
The pull process in The Welkin Suite works not as a "force-refresh from organization", but it ensures that you're working on the latest versions of file that were available on the organization. Since there are no changes on the organization, the IDE doesn't recognize a file changed and doesn't pull it.
At the same time, you can use a Local History functionality to restore your file to its previous version.
Also, can you please tell me what error you get when deploying your objects? Is this related to TWS errors or these errors are returned from Salesforce?
If this is related to the IDE, I kindly ask you to send us a bug report directly from the IDE so that we could get your TWS log files and analyze them to find a reason. Please file the option in the menu Help -> report a Bug, put your email and enable an 'Attach File Log' checkbox.
As for deleting files from a project, you can do this using the Project Metadata Components Wizard instead of removing a file from your drive since when you delete file manually in your local system - this file still is present in a project file (as well as the hashsum for it - the IDE uses hashsum to detect if there are any changes to files and if they need to be pulled).
If you would have any other questions, please let me know. I'll be happy to answer them.