Ran

aptly publish repo -architectures='amd64,i386' -passphrase='secret.' master_google-main master_google-main

It generates the following error:

Loading packages...
Generating metadata files and linking package files...
ERROR: unable to publish: unable to process packages: link /root/.aptly/pool/12/9a/google-chrome-stable_60.0.3112.78-1_amd64.deb /root/.aptly/public/master_google-main/pool/main/g/google-chrome-stable/google-chrome-stable_60.0.3112.78-1_amd64.deb: no such file or directory

Yes, the file google-chrome-stable_60.0.3112.78-1_amd64.deb is indeed not found.
but when I ran

>find . | grep google-chrome-stable_60.0.3112.78-1_amd64
./data/.aptly/pool/12/9a/c54d87724b58ea5cff53b05a4858_google-chrome-stable_60.0.3112.78-1_amd64.deb
./data/.aptly/pool/9a/64/c54d87724b58ea5cff53b05a4858_google-chrome-stable_60.0.3112.78-1_amd64.deb
./data/.aptly/public/master_google-main/pool/main/g/google-chrome-stable/c54d87724b58ea5cff53b05a4858_google-chrome-stable_60.0.3112.78-1_amd64.deb

Everything is handled by aptly, there is no manual intervention.
Why there is a prefix hash in front of google-chrome-stable_60.0.3112.78-1_amd64.deb?
If I delete everything and start over, the same issue happens but might be other package from other mirror.

Context

1. I mirror http://dl.google.com/linux/chrome/deb/ stable main: aptly mirror ....
2. Copy mirror to local repository: aptly repo import -architectures=amd64,i386 -with-deps=true google-main master_google-main Name
3. Publish local repository: aptly publish repo -architectures='amd64,i386' -passphrase='secret.' master_google-main master_google-main

Your Environment

aptly version: 1.0.1 or nightly build has the same problem.
Debian GNU/Linux 8 (jessie): 4.9.0-0.bpo.3-amd64