Say I have day traded some 3 script & profited Rs.1000.
And, had booked profit of Rs.500 on one of the long term Holdings Now, the positions shows a total profit of 1500.
Now, other things remain constant, the price of long term Holdings raise sharply so positions now starts showing a loss. I find this confusing. I have actually booked profit from my buy price in Holdings but in positions it’s a loss.
I don’t know what’s the best solution here. May be separating the day trades & non-day trade ones messy be an option.
Also, how does this reflect in p&l of end of day in q back office?
And for 60 day challenge?
Nice & noble @nithin please wave your magic wand 
Check this answer
P&L on Q will show intraday and delivery separately. For 60 day challenge, only buy/sell trades that happen within the 60 day period considered.