5 Short Books = Trilogy?

From the few agencies that I've looked into (but not yet queried) they like to have a word count with the query, or at least, a word count set for when they respond back to you with interest. Most would like to know what they're getting into, and I imagine, have an idea of something prior to investing into it.

50K is pretty low for a YA so if you continue to edit and combine two together, or parts of two with the first, then it would bump it significantly to a more suitable range.

I don't think you should query until you have a finished book which is as polished as you can get it to be. Turning 5 books into 3 sounds to me like you'll have quite a bit of editing to do to make sure the books stand alone and the pacing works. My suggestion is to stop querying until you have a polished, updated version of at least your first book. Then you can query and say it's a stand-alone with series potential. I wouldn't leave out the word count either, that just sounds like it'll irritate the agent.

^What PutPutt said.

When you query you'll be querying the first book only. So get that finished and done, then query it. Don't try to sell the whole series in that query: just focus on the first book. You can briefly mention that it has series potential, and at a push you could say that the other two to four books in the series are nearly complete: but don't try to query the whole series in one go. Agents will only want to consider one book from you.

As for transforming five books into three: that's a lot of work. You'd have to completely rework the story arcs and plots to make it work. If I were you I'd probably revise and polish as much as I thought the books needed and then consider if the lengths were appropriate; and if not, consider adding more to them--not waffle, real, strong plot. I think that would be easier than mashing them together.

Are you sure you are making the best use of the word count you have? Perhaps there are a few sub plots you can weave into that to make the first book more novel length?

Otherwise, all the above advice about getting the first book up to scratch is valid... they like a completed first novel and indication that you at least have an outline/idea for book two.

What's been said above. Never query until you're 100% DONE with writing. We've had so many stories on here from people who queried half-finished and mostly-finished works, only to find themselves up a certain creek sans-paddle when the agent turned around and said "Sounds great! Please send me your manuscript to review!".

Make your work as good as it can be before querying. If that means reworking the five books into three, especially if you can do so in a way that leaves the first book tolerably stand-alone, then rework away.