It seems that you put your message on the title so it is too long to be displayed. The latter half is cut off so I only see couple questions.
1. SR2 is different between S25FL127S and S25FL128S. From looking at your questions, I think you are using S25FL127S.
2. Typically, you should program SR2 bit before any program or erase operation. Because this bit changes the sector size, if it is programmed afterwards, some memory locations may not be the same as before.
3. However, if you don't care about the previous data, you may erase all sectors again after you program this bit. The device should be ok. You did not break it.
If you have any more questions, please write them in the message body, not the title, so we can see your complete questions.