Details
With replace option an Assembly disappears after searched by Where Used in structure editor
Solution
This is working as designed.
Top-level assembly file replace is nothing but opening a new file.
This is not a bom line (Assembly).
Replace should be used as follows:
1.Open an assembly
2.select one of child
3.replace it with other child component.
Notes and References
IR 9142640
Hardware/Software Configuration
Platform: INTL64
OS: window
OS Version: 764
Product: SOLID_EDGE
Application: DOC_MANAGEMENT
Version: V109MP15
Function: SEEC
Ref: 001-9142640