You may run following method to quickly check integrity of binaries in the database against filestore (assumes that you have a single filestore, such as shared NFS)
1. Get a list of binaries from Artifactory's database by querying sha1 values from "binaries" table
a. SELECT sha1 FROM binaries Order By sha1 ASC;
b. save the output as a file
2. Get a list of binaries from Artifactory's filestore.
b. Run following command
find . -mindepth 2 -type f -printf '%fn' | sort >> binaries-in-filestore.out
3. Find the differences between the results above using your favorite diff tool