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So I'll propose a solution, only hoping that the mechanics in your version are the same. Essentially it is this: specify the class of each ship, for which Fleet Manager is the right tool. Once the class is specified, they never get mixed up. If you don't specify the class, the AI makes its own defaults.
I have had a similar challenge with every other kind of ship (vettes, cruisers, etc.), and this is what I do. I also have several classes of each ship type. Early game I have a mix of gun and missile corvettes. From early to late game I make then change then toss all sorts of kinds of cruisers and eventually stop using anything smaller than them. And I'll have at least three kinds of battleships in each fleet. I design them, build them, and upgrade them retaining my fleet paradigm.
If the nanite interdictor ships (NIS) work the same as the rest, the same method should help.
In ship designer I design several kinds of, say, cruisers (let's call them RR). One is for missiles, another for neutron launchers, and a third for torpedoes (I'll call them M,N, and T), each with complimentary weapons to fill in. I give each a UNIQUE NAME (e.g., RRM, RRN, RRT... I can get quite complicated making various builds). That "unique name" becomes what Stellaris calls its "class," while the "ship type" is a cruiser (its hull, I guess). Now, let's say I have one fleet of 10 cruisers, like when I integrate an AI empire. I have to break that one fleet up into three different fleets - one for M, one for NL, one for T. Then I upgrade each individual fleet to that model, so now I have three tiny fleets, for example one fleet of 4 RRM's, another of only 3 RRT's, and the last of just 3 RRN's.
When that is done, I can put them together or into my other fleets. Thereafter, if I upgrade the whole fleet, each boat gets upgraded according to the UNIQUE NAME ("class") of that boat. The RRN's stay RRN's for the rest of the game unless I change them.
I'm an avid user of the fleet manager. People hate it, I understand; but I learned how to use it and, with a few defects and limitations, it's great. In fleet manager, I can pull up each fleet, and there I see that I have, say, a fleet with 3 RRM's and 6 RRN's. If I upgrade, I remain with the same 3 and 6. But if I want three of those RRN's to become a different class, like a RRT, I have to separate three into a new fleet of only three RRN's, then go into fleet manager, click on the little wrench next to those ships, and retrofit the three cruisers of that fleet to all to become RRT's. They do, and then I reincorporate them into the original fleet, and never again do my M, N, or T's get changed or switched into a different class.
That was long, and I'm only hoping I understood your question. I hope it helps.