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I suppose then your input is not tab delimited, try:-
awk '
NR == FNR {
A[$1] = $0
next
}
$1 in A {
split(A[$1], T)
...

for file in *.fa;
do
awk '
NR==FNR {
if ($0 ~ /^>/ && why_print_seqlen_for_this_line) {if (seqlen) print seqlen; next;}
# is there a record separator /^>/ in the *.fa files not...

awk '{ a[$0]} END{for (i in a) print i ORS}' RS= my_file.fasta
or better yet:

awk '!a[$0]++' RS= ORS='\n\n' my_file.fasta