paired reads have different names BWA MEM after samtools bam > fastq

Question

[robert.murphy]

I have used bwa mem to align to a host genome and output the unmapped reads. I have then sorted this resulting BAM and split into pairs fastq files. Whya fter sorting the BAM file am I still getting paired reads have different names error from bwa mem and can I solve this without resorting the fastq file itself?

[ATpoint]

R1 can align, R2 cannot, the new fastq files would miss the R1 name for that read and boom -- out of sync. You probably want to resync/repair it with something like repair.sh from BBMap suite.

[robert.murphy]

So there is no way to fix this during the conversion?

I have read that such repair tools can lead to data loss, is this not the case?