You can schedule re-scan of all data on your Bitbucket with a single REST-call like this:
curl -u admin -v -X PUT -d "" -H "Content-Type: application/json" http://bitbucket.server/rest/security/latest/status/total_rescan
admin is your Bitbucket admin user (you’ll be prompted for a password) and
bitbucket.server is URL of your Bitbucket server. You can monitor progress of scanning on Security Scan Report page.
Please note, that if you have much of data on your Bitbucket instance, all existing branches in all projects and repositories will be scanned, which may be very resource-consumptive and may take a long time to complete.
How to change the amount of parallel scans?
To optimize the load, you can try to change number of parallel threads used Security for Bitbucket during rescan with an additional REST-cal:
curl -u admin -v -X PUT -d "" -H "Content-Type: application/json" http://bitbucket.server/rest/security/latest/status/active/4
This command will change number of scan threads to
4. As of performance considerations, you cannot set number of threads greater than number of available CPUs. For maximum performance, you can specify 0 value to use all available CPUs, but be noticed that this can affect overall Bitbucket server performance dramatically.