I tried finding an answer by searching, but in vain.
If we flag a comment or a question, do we lose rep pts.?
No. You do not lose reputation points for flagging.
Correctly flagging helps the site and is even encouraged. You start out with 10 flags and you get more flags according to the following rules (from the help centre):
When you start out, you are allotted 10 flags per day. This number may increase to up to 100 flags per day:
- You get one bonus flag per 2000 reputation.
- You are awarded additional bonus flags when you flag correctly - one bonus flag for every ten net helpful flags (helpful flags minus declined flags).
Flags do not cost reputation. We do not want to discourage flags in any way, except when they are misused.
As others have stated, flags cost no rep.
But, as a counterpoint to encouragement to use flags, you should probably be using up your daily allotment of votes on qs and as well before you get to the flag limit. Same for voting to close (in both directions). That is,
upvotes > downvotes >> votes to close >>> flags to mods
where each extra '>' means a lot greater than). That flag limit is for the rare instance for an extreme situation, not the average. You want to hit your upvote count everyday. You don't want to expect to hit your flag max any day unless something really bad is happening.