Is it possible to re-align of SAM/BAM files?
Looks like I solved it by using PICARD: extracting the aligned reads but without sorting, I used 

java -jar picard.jar SamToFastq I=&lt;file_alnMAP.bam&gt; FASTQ=&lt;filemap_1.fq&gt; SECOND_END_FASTQ=&lt;filemap_2.fq&gt;
bwa mem -R &lt;read_group&gt; &lt;ref2.fa&gt; &lt;filemap_1.fq&gt; &lt;filemap_1.fq&gt;


From samtools flagstat the output looks fine.