If you right-click on HAL_QSPI_MODULE_ENABLED (at line 240), and then Go To Definition (F3, or via Right-Click menu), does it take you to that definition in stm32h7xx_hal_conf.h ?
Have you tried rebuilding the Index ?
In the Project Context menu:

@yilmazkircicek wrote:
2, 3 - I can see file icon on the top left corner of the stm32h7xx_hal_conf.h file name and context menu shows absoulte path when mouse over while other files path seems relative to project directory.
Not sure what you mean by that.
Show an example where you think you're getting "relative" paths ?
PS:
The indexing/referencing/shading is standard Eclipse stuff - not specific to STM32:
https://mcuoneclipse.com/2012/03/20/fixing-the-eclipse-index/
A complex system that works is invariably found to have evolved from a simple system that worked.A complex system designed from scratch never works and cannot be patched up to make it work.