[Genome] effect of using masked database

[Mera Vigyan]

Good Morning

I have been using BLAT for placing reads pair sequences of  a species of
grapes on the
full sequence of grapevine.  As a variation, i ran BLAT leniently with a
chunk of 50000
such sequences on the masked version of grapevine sequence.

my command line :

blat -stepSize=5 -minIdentity=0 -minScore=0 -out=blast8

I have some questions here :
1.Does running BLAT against a masked version of reference sequence help to
understand more
clearly the nature of structural variations and presence of transposable
elements
or running BLAT with masked version of query sequences against the actual
reference sequence
enable to understand them in a better way.

2. I also notice, the output relative to the chunk of 50000 sequences was
only generated for
49966 sequences. Why is this so ?
How can i get the output for the full chunk in such cases ?

thank you