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I'm losing the plot here. Could you please show an example or two of:

$fldr;
$f_name;
$f

One of the problems I'm having is that if $fldr has values such as

long_john_silver
...

How about this;

for fldr in ./folder1/* ; do
basenm=${fldr##*/}
if [[ "$basenm" = *_* ]] && [ -d "$fldr" ]; then
new_fldr=${basenm%%_*}
if [ -d...

man bash:

find . -name *fna.gz | while read f ; do fl=${f%/*}; fld=${fl##*/} ; echo mv "$f" "$fl/${fld}_${f##*/}" ; done
Test first. To perform rename, update as needed then remove echo