Sometimes some trackers are merged into a new one.
For example HD-City and HD-Spain were merged and the newborn was Pixelados.

How is this process done from a technical point of view?
How are the databases merged without affecting to all the clients?
How does it affect this process to the "leechers" that are in the process of downloading a file?

The databases could be merged the same as most databases, the problems I see would be the passkey and announce URLs.
I've never seen it happen but I imagine the easiest way would be to merge the user lists and give everybody a new passkey, then reconfigure the tracker that is going to be used to use the new announce URL and have everybody re-download a bulk batch of the previously downloaded torrent files, which thr user would need to manually aim at the respective downloads. You could probably also just leave the prior downloaded torrents to use the old announce urls and then make a new tracker which monitors the old 2 and updates the user's ratios on the new 1 based on what gets reported - but that's probably not likely