Hi Shirley
Regarding your 1st question, it is recommended not to substitute ئ with ی as they are different letters and they sound differently. This substitution is a common mistake as they look similar and the former character has been directly borrowed from Arabic. Therefor, it is رئیس and not the other way around.
And with respect to your 2nd question, the short answer is yes you can. However, it sounds more natural and native-like to use their Arabic counterparts. At least, for the aforementioned words. Thus, دلیل ها as well as منبع ها and ساحل ها is acceptable.
Best
Ehsan