After installing version 6.61 the linking window is not fully visible

I’m unable to reproduce what you’re experiencing on a WordPress 6.6.1 with just the default Twenty Twenty-Four theme and no plugin active. In fact, I’m not even sure I fully understand your description.

Below is what I see when linking text in the default block editor. Can you provide a screenshot depicting what you’re experiencing?

I use the 2022 theme.
Below is the effect when linking and editing the link:

As you can see, the linking dialog partially hides at the end of the blog post area.

With the first few dozen lines of text, the linking dialog box appears in its entirety and works without problems.

The problems begin when we enter a lot of text and its last line is directly above the edge of the text entry area. Then the linking dialog box appears, for example, only showing one line for entering the link, and the remaining options are no longer visible. As I wrote, a temporary workaround for this problem is to add 5-7 newline characters so that there is artificial space for the linking dialog box and it does not hide “under the surface” of the area beyond the space for the text of the entries.

In my example, I added only 2 empty lines and then the linking dialog box partially appeared.