I have a head-tail duplication with a big retrotransposon at the boundary of said duplication. However, all introns are maintained in both gene copies. Is it possible for retrocopies to maintain introns despite undergoing transcription and then subsequent reverse-transcription? Thanks!
Yes, there are two major classes of transposons; class I (retrotransposons), and class II (DNA transposons). So, yes, it is possible by DNA duplication.
It's certainly possible for a retrotransposase to grab onto any RNA and reverse-transcribe it back into the DNA sequence. However, in order to retain introns, the RNA would have to be unspliced or partially spliced, which is possible. However, when you say "all introns are maintained" my interpretation is that this will not match a known isoform, and so I would be skeptical that a retrotransposon was an origin of the event -- instead it was likely mediated by a different DNA-only mechanism.
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While I don't think this is necesarilly a bioinformatics question, here is my 2 cents: Yes, there are cases where non-homologous recombination happens thanks to repetitive DNA (like retrotransposons), so it wouldn't be weird to assume that this is the case, but hard to tell without careful examination.