I think this is the reason for making a clean break at a certain moment. There's no advantage IMO, and it is much harder, to move some images from Catalog A into Catalog B first, and then to move others later.
If you did want to do that, the means of doing that would be to highlight some images in A, Export as Catalog to a new intermediate Catalog X, go to B, Import from Another Catalog selecting to merge in the contents of X, review that it's worked, go back to A, remove (not delete from disk) the highlighted images, delete intermediate Catalog X.
As opposed to: in A higlight ALL the needed images, Export as Catalog B, remove those images from A.
If there is a difficulty in identifying which images should be highlighted for inclusion, then the priority should be IMO to progressively add metadata or labelling of some sort, until everything is suitably discriminated. Note that this process does not require physically moving any images into another folder. And then you can do your clean break all in one go.
There's no technical difficulty in having some images even within the same folder imported to one Catalog, and others to a different Catalog - though there can be confusion from some images being imported to both, especially when edits are being written out as external metadata, from either Catalog (or from both).
The methods described above all just involve re-referencing files that continue to live unaffected wherever they are.
If there is also a desire to separate the physical locations of files imported to Catalog A, from those imported to Catalog B - for example, if these will have different storage / backup requirements - then copies of the files, retaining all their relative arrangement into subfolders, can be made into a separate location as part of the Export as Catalog procedure. This is done with a checkbox in the Export as Catalog dialog, "Include Originals" (or "Negatives" iirc). It will then be these new file copies that get referenced by the newly made separate Catalog B, not the files that Catalog A is still referencing. Then the cleanup of these images out of Catalog A may include not just Removing theem, but also Deleting from Disk (to avoid doubled storage of these files going forward). Obviously this more radical option requires a lot more care, and so should definitely be supported by up-to-date full backups to other media of everything: image files and folders, and Catalog(s).
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