Hi, I lost my download counters as well but I notice something.
It did count/updated the downloads count numbers only with the log records count. In the past versions on log reports we had the option to delete the logs, that was something I did a few times to clean some records that I did not use and was a big chunk of my database.
The old download counts are still in the _postsmeta table as metakey: _download_count. I solved my problem migrating the old numbers into the new dlm_downloads table matching the ID value.
I think the DEVs must migrate the counter from _download_count meta_key numbers instead gathering only from the log records to prevent the counter to get messed up in cases that the user has cleaned up the log records prior update.