I did a clear history and website data in Safari and now all my bookmarks are gone

Clearing history will not delete your Favourites/Bookmarks.

You may find this article to be helpful in understanding some of the frequent difficulties encountered by users new to iPadOS Safari - along with some of Safari’s more esoteric features and quirks:

iPadOS - Safari - Lost Windows, Lost Tabs… - Apple Community

Insofar as possible, I hope to have distilled most of the frequent problems reported here - and documented procedures, strategies [and where needed] some useful workarounds.

Hmmm, I just tested that on my iPad Pro: cleared all history and website data on it; launched Safari, hit the bookmark sign in upper left and not only are all the bookmarks there, but all of my tabs are still showing in the tab bar:

I was signed out of ASC, but I expect that and will need to sign into all the sites, but the bookmarks are there.

Have you tried tapping the bookmark sign to see if they show up?

And, are you really on iOS 9? I am on iOS 14.x, so there may be a difference there.

Edit: never mind, missed that you are on the latest iOS - so there shouldn't be a difference.

You deleted that data.

Only if you have a backup that includes it.

Very, very old iPad that can't be updated.

They mistaking cleared the browser data.

Look at the OP's post - they say they are on the latest iOS and I cleared the history and website data without losing my bookmarks.

I'm confused as they have iOS 9 in the iPad profile.

Either way they made a mistake.