Microsoft Project Integration Manager prompts user about overwriting a project or task. The message that shows up is There is already a task with the name “Design Evaluation” at the same level in Web TimeSheet. Select “Yes” to overwrite this task with task having Unique ID “1” and name “Design Evaluation” in MS-PROJECT. Select “No” to skip the update for the task which will have the task unchanged in Web TimeSheet.
When a project is transferred from Web TimeSheet to MS-Project or MS-Project to Web Timesheet, it creates a mapping between the objects in both Web TimeSheet and MS-Project based on various id's in both systems. The project should be created in one or the other system – not both – and transferred into the other thereby correctly creating the mapping. Edits should similarly be made in one system and transferred to the other – if they are made in both when the transfer is done there may be disjoint data that needs to be overwritten to correctly complete the mapping.
So this issue could be related to edits done in both systems and if you select to not overwrite it probably doesn't update the mapping. But it could also be an issue with multiple sets of the project file causing id and sync issues.
Need to re-save all the affected projects using the Save As within MS-Project to have new copies of the files created with correct unique id’s and then re-transfer them to Web TimeSheet. After they've been re-transferred and the mappings created correctly this should probably solve the issue. And any further projects that need to be created from the template should have the template loaded into MS-Project and then the new copy created via Save As.
For file MyProj.mpp in MS-Project and project MyProj in Web TimeSheet.
Rename MyProj.mpp to MyProj_temp.mpp
Load MyProj_temp.mpp into MS-Project and save as MyProj.mpp (which assigns a new ID in the MPP file)
Upload MyProj.mpp to Web TimeSheet, and integration tool prompt you to overwrite the existing project (since the MPP has the new ID)
At this point, the MPP file and Web TimeSheet project are properly associated by ID such that integration tool uploads/downloads work properly.