The problem is that PSoC Designer 5.1 doesn't support projects created on PSoC Designer version earlier than 4.4. Steps for how to clone old projects to PD5.1 are below:
1. Open your project in PD4.1 (or whichever PD version the project was originally built in), and rebuild
2. Open your rebuilt project in PD5.1
3. Unplace all UMs and build. There will be errors, please ignore them. Close project.
4. Create a new PD5.1 project. Choose a name and select "Clone project". Select the Project which was created after step 3.
5. Choose Target device and hit OK.
6. PSoC Designer 5.1 will delete all unsupported User Modules. You must then place all necessary UMs manually.