This looks like a problem internal to the binary package (*.deb) itself, unrelated to reprepro. (Almost) every binary package contains an md5sums file in its control component. You can take a look at it wth:
ar -x qualys-cloud-agent_2.6.0-88_all.deb # extracts {control,data}.tar.xz
tar -xf control.tar.xz # extracts control,md5sums
cat md5sums
The best solution is to release qualys-cloud-agent_2.6.0-88.1 which is a simple rebuild of 2.6.0-88. Before you dput it, install it locally and verify the md5sums with debsums (from the debsums package).
dpkg -i qualys-cloud-agent_2.6.0-88.1_all.deb
debsums -c qualys-cloud-agent
If the check passes, you can dput <your_repo> qualys-cloud-agent_2.6.0-88.1_all.changes.
It's important to bump the version of the package because it'll ensure anyone who has installed this package from your repository gets the update. If you really don't want to bump the version (maybe you are certain no one has used your repo); you could:
reprepro -Vb /path/to/repo remove buster qualys-cloud-agent
reprepro -Vb /path/to/repo include buster qualys-cloud-agent_2.6.0-88_all.changes
If the debsums fails, it would be useful to:
- know how you built your package (
dpkg-buildpackage, cpack, dpkg-deb)
- see an extract from
/var/lib/dpkg/info/qualys-cloud-agent.md5sums so we can look for any formatting problems
- know if you are using
reprepro includedeb instead of reprepro include