This seems highly improbable to me, assuming that 'keep settings' was not used (unchecked via LuCI or '-n' argument on the CLI). When the flash operation is performed, nothing is retained. So it makes no difference if you are upgrading from a previous version or cross-grading between targets (or both simultaneously). IMO, what is more likely is that it was a configuration error (either retained due to accidentally having 'keep settings' enabled or something added/omitted or some other typo during the re-configuration process).
FWIW, I upgraded my RouterStation Pro from 18.06.5 (ar71xx) to 19.07.0 (ath79) directly, reinstalled packages, and then transferred my configuration manually (selectively) back into the RSPro. Everything worked perfectly when I had completed the process.
I was very careful and selective about what files I copied directly as well as those that I copy/pasted sections, and I did not move any files that were not directly relevant to my configuration. All files that planned to touch were carefully reviewed to ensure compatibility. I found that it was safe to simply copy (scp) many of the non-hardware specific files (i.e. firewall, dhcp, openvpn main config file, etc), but the /etc/config/network file required manually editing the configuration (including my network IP declaration and copying the OpenVPN and WG related interfaces over, but using care to not edit/replace the majority of the file with the previous configuration details). It would be easy to introduce a typo or some other minor configuration error by mistake, or to omit the installation of a specific package. But, if approached with attention to detail, there is no reason to suggest that the upgrade+crossgrade was the source of any issues.