I think you will have to first identify the regions homologous to the ones defined in your GFF and then transfer the annotations. Of course, the assumption there is that the homolog will also have the same annotation which is often not true. However, I don't see how you can do it in any other way since you cannot use genomic coordinates (and you would still be making the same assumption even if you could, anyway) when the genomes are so different.
For a very simplistic approach (which might be enough if, as you say, your sequences are almost identical), you can do something like:
- Collect the sequences of interest from your already annotated species.
Use a tool like
exonerate to map these into the target genome. Both tools can return gff-formatted output and both can find multiple hits in the target genome. For what you want, I would suggest using a very high threshold of sequence similarity and query coverage (where the target sequence found covers all or most of the query sequence used).
Since these are microbial genomes and therefore splicing isn't a problem, you could do the same thing with even a simple BLASTn or tBLASTn if you start from protein sequences.
At this point, you should have a list of homologs (some of which will be orthologs and others paralogs) and you can transfer the annotations of the query sequence over to the target.
Again, I stress that this is making a whopping huge assumption: that homologous sequences have the same function and can automatically be annotated as whatever you had in the query genome. This is going to be true for many cases but it will also be false for others. Especially if you are looking at paralogs (genes whose duplication occurred after the speciation event and are therefore likely to have diverged in function).
However, as I said before, this problem would be exactly the same even if you did manage to transfer annotations just by identifying the syntenic regions of the genomes1, so there's not much difference there.
1 As I said in the comments, I don't see how this could be possible. By definition, if you have extensive duplications, the genomic coordinates will be completely different and it is impossible to map from one genome into the other.