Loss of Identity: Given how often it’s done (see: Body Surf), everyone in a modern transsophont civilization is pretty clear that body-swapping doesn’t cause it. The mind is not the plaything of the body – fundamentally, at least, even if it may distort the way it plays out.
Strictly speaking, say the Empire’s sophotechnologists, identity could be defined by the logos, the personality organization algorithm, alone. It’s the unique, volitional, free-will-granting thing, after all – but that’s much the same standard as reincarnation might be said to use; sure, it’s the same soul, but when you throw away all the memories and personality…
Thus, for practical purposes, there are legal standards concerning exactly how much of the mass of archetypes, subpersonalities, personae, agents, talents, memes, memories, etc., etc., that make up the rest of the mind you can grossly edit or remove over how much time before you are no longer, in the eyes of the law and (practically speaking) everyone who knows you, the same person. To avoid committing de jure cognicide on yourself, stay on this side of the line.
Instant AI, Just Add Water: Was once true in the old days, back when people were quite often using mental modules scanned, compiled, and tweaked from brain-scans of biosapiences in their AI architectures. The logos/personality organization algorithm is pretty damn resilient, and often such inexpertly designed modules carried at least a chunk of it along with them in the scan, and it doesn’t take much for it to at least start a self-development cascade.
But they’re much better at mental architecture design and coding from scratch these days, and don’t let logoi creep in unless they actually intend for them to be there.
(The “if you wake up, please call this number to let us know and claim your sophont rights” code-package is still included in all AI seeds just in case, though.)
Ghost In The Machine: Averted. Souls are software objects; there are no supernatural qualities whatsoever to sophont life, and even if you can pull out the software, recompile it, and stick it in another body, the only thing that’s being transferred is data.
It would always be possible to consider the logos/personality organization algorithm, the weird non-deterministic chunk of mathematics that appears to produce volition as something of this sort, I suppose; or in a weak Cartesian-theater sense the consciousness loop, even if all it does is organize your cognitive processing into a narrative thread, and it’s entirely possible to build minds without them if you’re okay with the resulting weirdness. But in no case is there any ghost present; it’s just the “program in the machine”.
(That all being said, of course, when asked geth-type questions like “Does this unit have a soul?”, the Imperial answer is unambiguously yes. Inasmuch as “soul”, in modern sophotechnologist jargon, is slang for “personality organization algorithm”, which is to say, that thing which makes you you.)