The default Ajax Filters that come with nopCommerce are already styled for the Venture theme so you can use them instead of our Ajax Filters plugin.
We have made them to look pretty much the same as our Ajax Filters so probably you don't notice the difference.
Anyway simply update the theme and you should be able to use both.
If you have followed the documentation this means that you have done only changes that are persisted to the database i.e configuration changes to the Plugins like creating a Slider etc.
So all the changes you have done will be automatically available in 4.4.
If you have done modifications to the theme files i.e .cshtml files then you would need to make these changes again in 4.4.