Thank you for your bug report.
The reason for the issue you are faced with is the exceeded Salesforce limit of files that can be included to one request.
TWS sends such requests to Salesforce with the set of your metadata files to check them for updates on the server. Each of them is related to the separate metadata type.
Can you please reproduce the issue and send us the bug report directly from TWS right after this? This option is available for you in the Main Menu -> Help -> Report a Bug. You can paste the link to the current topic as a description, and please make sure that 'Attach Log File' checkbox is enabled.
I kindly ask you to check if some of your metadata types contains more than 2000 files. If this is acceptable for you, please pull these files part by part.
Our developers will investigate the ways to handle this case to avoid the error related to limits.
The error wasn't present during the project creation because in this case files were downloaded to the IDE and no related requests were no sent to Salesforce.
If you have any additional questions, please contact us. We will be happy to assist.