Prendre congé has the meaning of asking the permission to leave (duty, employment, but also a social gathering, etc.) and thus in the context of instructions about writing a letter means terminating the letter. Traditional French etiquette is very formal for that (see this answer for links).

For an email, those instructions seem much more formal that what is usual.

I see that Google Translate, just like everyone, has a problem with “l’y”…

“Take leave” is the correct translation for “prendre congé”, but in this case (an e-mail), a more topical wording would be “conclude with greetings”.

As for the first part, the “l’y” part hasn’t been taken into account, and it doesn’t make sense without it. See if this is sound better to you: “Say you hope to see him/her there”.

Notes: the instructions use formal language, which doesn’t quite mix well with e-mail…

“Prendre congé” means “to leave an assembly, a reception, etc.” , usually with some words of greeting or thanks, but not necessarily.

“Prendre un congé” is official, and granted for holidays, maternity, studies, etc., for a fixed delay.

It is the origin of two funny expressions.
At the Spanish Court, in the XVIth century, you had to salute every single person of an assembly when leaving.
The French thought it was somewhat too formal and boring to just pay some respects for the hostess, for instance, and the Spanish invented the “Disperdirse a la francesa”, promptly translated in English by “Take a French leave”, without any tint of real reproach, because in fact everybody thought it to be reasonable.

The French then understood wrongly this, coming from the Perfid Albion, as “nicking off”, and took revenge in translating back by “filer à l’anglaise”, which is always pejorative.