Flash memory to hold flags
Assuming a NOR flash you have to erase entire sector everytime when you have to update the contents of it, even if it is. Single byte.  

If the bootloader seldom does the wrote operation, it is okay to reserve the whole sector to store your flag. When you need to clear it, you have to erase the whole sector and wait until it is complete.   

I would like to also add that, please take care to see that the maximum number of allowed flash erase operations isn't crossed.
You can find that information in the datasheet.  Probably I would not cross not even 10 percent of what datasheet claims as maximum supported number of flash writes/erases.