How to transfer gff annotations in genome with extensive duplications?
There is one very simplistic way I use which might work for what you are doing, it is similar to what terdon proposed.

Take a de-novo microbial genome annotation tool (I have my own, but you could use/modify prokka). Tools like these often first predict gene boundaries (with other tools like prodigal or glimmer) and then try to assign a function to found genes. This function assignment is often done with BLAST and other tools ... and that is where you can go in and modify to do what you need.

I use a "knowledge" protein database of genes I want to have very strictly annotated as a first line of annotation (e.g. in your case: the annotated genomes). For that I loop through very strict identity/similarity parameters which get gradually relaxed.

E.g.:
Loop 0: only transfer annotations at 100% DNA identity, same length.
Loop 1: only transfer annotations at 100% similarity, same length.
Loop 2: only transfer annotations at 99% similarity, length +/- 1%.
...
Loop n: only transfer annotations at 100-(n-1)% similarity, length +/- (n-1)%.

In each loop, obviously only annotate what has not been annotated in previous loops.

After that, use "normal" annotation pipeline of the tool to annotate the rest.