Speaking from a slightly technical viewpoint, I wonder what would happen if Funcom tried this:
During a downtime, they go into the database that keeps track of all renown for the weekly charts and just 0 everything out. This would be 0 renown gained of any type for all guilds/players. They would also 0 out the previous weeks data to insure there are no old numbers creeping in. A person looking at the rankings when the servers pop back up would see basically an empty list. You would think if they did this, and there wasn't a really big problem elsewhere in the code, then rankings would start to update regularly again.
Makes me sort of wonder what the problem really is. With it happening when the servers were merged, you would think it was caused by something that changed during the merge. So, thinking on what must have changed, I come up with Guild Chat ID's (Not sure if these are the same as the guild ID) and Player ID's. (and other ID's like a server ID maybe)
Guild Chat ID's didn't seem to change all that drastically, nor did player ID's.
Guild Chat IDs:
12884922556 - old (I think)
12885333191 - new
Player:
17270730 - old
61305864 - new
I wonder if the ID's being used by the renown system didn't get updated properly in the database, which caused things to get out of wack and stop working...
I just have to imagine the logic code behind the Renown system shouldn't have broken by itself with the server merge, so it would have to be a data issue. Corrupt data causing the system to fail to function properly. If you have bad data, clearing it all out and starting over would usually work.