This is a known issue in PD5.0 SP5 that does not allow you to reopen a system level project if it was not built before it was saved. As a workaround, please take care to build the system level project before you save it.
This bug has been fixed in PSD5.0 SP5.5. Upgrading to the PSDesigner version 5.0 SP 6 will solve this issue.
Note: PSoC Designer 5.0 Service Pack 6 is the last release of PSoC Designer that supports System-Level Design (PSoC Express). PSoC Designer 5.1 and beyond will not support System Level Design.