Creating a new reference genome B by changing genome A with mismatches from BAM file without long reads
You should be able to use something like Pilon to convert from one genome to another, assuming the changes are all fairly small local changes (but that's almost never the case).

I find your resistance to long-read data interesting. It's important to consider the cost of bioinformatics as well. Sequencing a phage genome with long reads will take less than an hour, and probably produce a few reads that cover the entire genome. With existing short-read data, those full-length reads should be able to be fixed up within a day.

I spent about half a year trying to fix a eukaryotic genome assembly that was assembled only from short reads (using Pilon, and L-RNA-scaffolder), and I was only able to reduce the number of contigs down by about half (and even at that, I wasn't convinced that contigs were being properly joined). With long reads and another couple of weeks of computer work, the contigs dropped down to about a tenth of their original number.

If you can use a pipette and have about half an hour spare, you can do rapid long-read sequencing on the MinION.