I have a project I have been working with successfully for weeks. Last night I added two referenced pacakges, both are Managed Packages produced by the same vendor.
I saved, shutdown, cam into the office this morning and opened the project to get the error:
Project is corrupted. Please re-create project.
Looking in the log file I find this error:
2018/06/04 06:56:33.284 [INFO]  TWS (126.96.36.199) has been started.
2018/06/04 06:59:21.515 [ERROR]  The files with id '01Ib0000000gY6rEAE' are duplicated
Sure enough, looking in my .sfproj file, I find that ID twice, once for each of the two referenced packages, though the first occurance shows the object name with the name space specified twice:
<Object Include="Referenced Packages\Amadeus Central Sales\objects\NICC__NICC__Booking__c.object">
<PhysicalRelativePath>Referenced Packages\Amadeus Central Sales\objects\NICC__NICC__Booking__c.object</PhysicalRelativePath>
<PackageName>Amadeus Central Sales</PackageName>
<Object Include="Referenced Packages\Newmarket Common\objects\NICC__Booking__c.object">
<PhysicalRelativePath>Referenced Packages\Newmarket Common\objects\NICC__Booking__c.object</PhysicalRelativePath>
I think the problem is occurring because the Object's original definition is in the "Newmarket Common" package. Then the "Amadeus Central Sales" package adds 3 columns to the original object (I've attached the two .object files that TWS created).
If I manually edit the .sfproj file to remove the NICC__NICC__Booking__c.object <Object> node, then the TWS project will again open correctly, though I don't know what negative effect this may have. Intellisense does still show the three fields that were added to NICC__Booking__c.object as part of the "Amadeus Central Sales" package. So I am (so far) seeing no negative effects to my manually modifying the project. Though I will need to do that edit every time I pull code if I pull the Referenced Packages