less reads mapped in proper pair with --split-prefix

[cocodsf]

Hello

I would like to understand why the reads are not(less) mapped in proper pairs when --split-prefix is used ?

with split-prefix (index .mmI < target size) (25% in proper pair)
minimap2/2.22 --sam-hit-only -2 -ax sr bqPART.mmI read1 read2 --secondary=yes --split-prefix tmp > map1.sam

read1 113 CTG819.1 104 0 101M CTG6.8 AS:i:202 tp:A:P

read2 179 CTG6.8 1106 31 6S34M3D37M2S CTG819.1 AS:i:124 tp:A:P

read1 355 CTG6.8 944 0 101M = AS:i:202 tp:A:S

index .mmI == target size (no split-prefix needed) (85% in proper pair)
minimap2 --sam-hit-only -2 -ax sr bqFULL.mmI read1 read2 > map1.sam

read1 99 CTG6.8 944 26 101M = AS:i:202 tp:A:P

read2 147 CTG6.8 1106 33 6S34M3D37M2S = AS:i:124 tp:A:P

Thank you for your help
Corinne