Thank you for your contacting us with this information.
May I please clarify with you if you saved all your changes in the custom label file locally before you have deployed them to Salesforce? In addition, can you please tell me if the labels that don't exist on the server are present in TWS?
If these labels are present I kindly ask you to save the file one more time and deploy it repeatedly.
In the case, if the issue is reproduced after this, please send us a bug report directly from the IDE. This option is available for you in the
Main Menu -> Help -> Report a bug. You can use the link to the current post as a description and please make sure that the 'Attach Log File' checkbox is enabled.
This will help us in the investigation related to the issue you are faced.