after implementing bootloader, main application hangs on HAL_Delay()

I f by activation you mean initialization

Then my bootloader activates all of the system peripheral,and it doesn't deactivates any other thing.

My main application starts performing after ONLY after a hw reset in any other case it hangs and then you have to give hard reset and then it works fine.

BUT why it stops only at the HAL_Delay and not any other statement.

I f by activation you mean initialization

Then my bootloader activates all of the system peripheral,and it doesn't deactivates any other thing.

My main application starts performing after ONLY after a hw reset in any other case it hangs and then you have to give hard reset and then it works fine.

BUT why it stops only at the HAL_Delay and not any other statement.

Don't develop boot loaders as if they are full applications. Only turn on what you need. And consider turning things off again before jumping to the app.

If the app has a code sequence that assumes all registers are in the hw reset state then the code can fail. Either because the code assumes a specific register can be left as is. Or because the order of the initialization can be dangerous if the boot loader have already performed the last steps when the app performs the first steps.