EDIT: I have not found a permanent solution yet but i discovered a way to dodge the problem. Im posting this in case someone with the same issue comes across this thread. If anyone has a better idea , please comment.
Never ever open psd files in sai. It fucks its brains and it cant save anything except of psd. Do not open psd files in sai. If u accidentaly did , close the program and re-open it before you start working on anything. Otherwise you are forced to save in psd. If you have a file that you had to save as psd but wanted to work on sai ( happened to me) all i can say is work with it in sai , save it as psd and then save it as an image in photoshop..this is ok i guess , unless your using masks or other more complex tools. In this case the one program does not support the tools of the other...so its important to keep the files seperate and pass them from one to another only if you are sure about it.