In recent years, anime studios have begun to air some series in what is known as a "split cour" format. This is where half of the series is aired one season, followed by a break (typically one season), followed by the second half. Up until recently, we have typically treated each "cour" as its own season on TheTVDB, however after some internal discussion and in an effort to apply consistent policies across as many series as possible, series like this will now be treated as a single season.

We already treat other, non-anime series in this way, although they are typically referred to as mid-season breaks instead. Some examples of this are some seasons of Breaking Bad, Futurama, South Park, Mad Men, and many more.

Another telling fact is that the official sites for most of these split-cour series list the episodes as 1-24, further reinforcing that this was always a single "season" with a broadcast break midway through.

We have made retroactive changes to some anime series that our moderators personally know aired in a split-cour format. 

At this point, this is a non-exhaustive list due to the split-cour format becoming more and more common.

Series Changed

Fate/Zero (S2 merged into S1)
Fate/Stay Night: Unlimited Blade Works (S2 merged into S1)
Durarara (S3 merged into S2)
Jormungand (S2 merged into S1)
Space Dandy (S2 merged into S1)
Aldnoah.Zero (S2 merged into S1)
JoJo's Bizarre Adventure (2012) (S3 merged into S2)
The iDOLM@STER Cinderella Girls (S2 merged into S1)
Mushishi (S3 merged into S2) - This one was done a while ago
Black Lagoon (S2 merged into S1)

Series Not Changed

For these series, the episode numbering (both on the episodes themselves and the official site), TV schedule information and several other resources all consider the second half to be a second season in its own right.
Chaika the Coffin Princess
Silver Spoon