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The .bashrc is a file the shell can source, it is not your shell history. Regardless I don't know any package that wipes your ~/.bash_history by default. If this happens I'd make sure to check with other users (if any) and check login records (last, lastb) and system and daemon logs for anomalies.
.bash_history stores the most recent 500 entries in the user shell. It can be edited manually be editing the ~/.bash_history file but should not be automatically cleaned out-- except for entries greater then 500. If you are finding your history to be emptied often I would be concerned about a rootkit, or a user who is doing something they are trying hide (which is potentially just as a bad as a rootkit).
As unSpawn said you should look at your logs and who has been logged in when--but this may prove difficult because if something malicious is going on log accuracy is suspect also. Start off by installing (if not already installed) chkrootkit and rkhunter (root kit hunter) Run both program and see if they find any problems. If they find a problem start there in your investigation as to what is going on but note that both programs have a level of false positives due to their purposes. The results should only be used as a start--don't delete files they find to be a problem without first investigating and verifying the problem.
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