Filtering through Main Drain without skimming

Since I need to dilute my CYA infested pool, I am draining down every day to below the skimmer and I am filtering through the main drain only. I am doing it gradually because I want to use rain water (I diverted one of my gutters) which has a pH of ~7.4 rather than my tap water (pH <6.8)

Obviously the floating debris will just circle around but other than that does this prevent any problems to operate like this for maybe a week? How long before not skimming starts to cause any problems?
 
Well it is going to be a lot longer than 1 week if I rely exclusively on rain to fill my pool. We are just not getting significant rain amounts and the rains have been really short in duration as in 5 or 10 minutes. I only took the water level down about 8 inches and in 5 days it still hasn't filled up. Its irritating because earlier this month the pool was overfilling and required multiple pump outs. This was before I diverted water from one of my downspouts into my pool. I may have to revert to well water if I want to get this CYA diluted any time soon.
 
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