So take this with a grain of salt, because it is anecdotal and I can't find the parcel fabric patch notes to support it, but I had this same problem in the past. I believe it was fixed in a more recent update of ArcGIS Pro because I haven't had this problem occur for a while. For reference, I am on version 3.1.3. Here is a multipart parcel from our fabric:
When I shrink it to seeds, it creates three seeds as shown below:
I then use the reconstruct from seeds button, and it rebuilds all three of them as one:
Make sure that all three of your parts have the exact same attribute information and they should be combined combined into one multi-part parcel. If you have the ability to, I would try and update to the latest version of ArcGIS Pro and then test it again.
Hopefully this helps!