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Try:
#!/usr/bin/gawk -f

BEGIN{FS=OFS="|"}

{
<do my stuff 1>

# need to remove empty fields at this stage

gsub(/^\||\|$/,x)
gsub(/\|\|/,FS)

# need to keep going with...

Yes x is a variable, and since it has not been initialized, it contains the value ""

You would need to do something like this to shift the fields:
awk '{for(i=1; i<=NF; i++) if($i=="") for(j=i;j<=NF;j++)$j=$(j+1)}1' FS=\| OFS=\| infile
output:
1|2|3|4|5|6||
But that still leaves...