Hi Judy, I too am in the process of moving over 10,000 names from Ancestry to WikiTree. I found the best thing to do is to create all new Trees following specific branches of my main Trees. For example, I started at myself and work up through my maternal grandmothers father back as far as I could go. The nice thing about Ancestry is the Ancestry Member Tree hints can be used as a cheat to fill in siblings, spouses, etc. Now this only fills in names and dates and birth and death locations. But that is what is important to the Ancestry Hint Search. Just be sure to only select your Tree as the Ancestry Member Tree Source as you are sure that data is good. Don't trust other Ancestry Member Tree Hints. I then go back and refill each persons records and sources using the hints. You always have your original tree to go back and check things. This is where you can fix any errors you think you may have and also if the person is someone you haven't worked on for awhile, there is probably new data for you to add. A bonus there.
When it starts to get around 400 names. I pick a family member as a stop point and end that tree with them. I then download the gedcom and load the new and re-verified tree to WikiTree. Then I start at the previously mentioned family member I used as a stop point and go on from there and create a new tree. I am doing this for each branch. Stopping in the middle of a branch is ok, you can pick up where you left off.
Sounds time consuming, but it really isn't overall and you get to revisit some family you may have not seen for awhile and correct any possible errors.. And the time saved when you load to WikiTree is well worth the time spent here..Just the possible error correction is worth it. Your new gedcom file is cleaner and more efficient. (Just remove the Ancestry Member Tree Hint as in the Source area for each name as it isn't really a source, more of a cheat.) LOL
The only real problem with this method is that you will find new data and you may want to start chasing that trail. If you can refrain from that and just stick to making your tree for a gedcom upload, time goes fast. Save those new trails for later additions. Sadly, I am an addict to new trails and I can't follow my own advice. LOL
Any questions, please contact me or just reply to this answer and I'll be notified.
Lee Russell