Reputation points are important. They dictate the various privileges which an individual's account has. Reputation is affected by upvotes, downvotes, deletions, and also your bounties. Loss of reputation amounts leads to loss of privileges, as we use reputation as a sort of 'privilege' gauge to earn permissions by having good contributions. As was posted in zaq's answer, reputation to some extent indicates:
levels of experience, familiarity with system/site, trust,
and some other things.
This risk of loss-of-reputation is documented in many places, such as these on the StackExchange Meta:
Let's take a hypothetical situation:
I am a user who has 2005 reputation, which means that I have access to review queues, etc. I get three downvotes on three answers, which means I'll lose at least 6 reputation points, which drops me to 1999 reputation points. I have lost the 2k review privileges. This is the design of the system, of course.
Let's take another hypothetical situation, one that is sometimes observed:
I am one of fifteen users involved in a voting ring. Across all fifteen of us, we have each managed to get over 3k reputation. We are discovered, and all the votes invalidated by moderators and community managers, and we drop down to 150 rep each. I've lost my privileges at the reputation levels of 200 through 3000, because I've had my reputation invalidated and revoked.
Or, let's take your hypothetical with some changes:
I am a 15k user, with exactly 15250 reputation. This gives me access to the "protect" function on some questions. I place a 500-reputation bounty, which means I lose 500 reputation. This leaves me with 14750 reputation points, which falls below the 15k threshold for the "protect" privileges. Unless something major happens that would revert that bounty, I have lost that privilege and need to 'regain' it by good contributions to the site.
This is simply the design of the system. The Bounty system help page even explains that the bounties can lead to loss of reputation and privileges when you make too many bounties and therefore lose enough rep to dip below a permission level.
Bounties aren't usually reverted, so you'll just have to regain your 2k privileges with good contributions.