\FILE04BUET-PCO;\SERVER24DFSSHAREDCORPETPROJECT CONTROL OFFICE;/FS7_150a/FILE04/BU-D/PROJECT CONTROL OFFICE;10000bytes;9888;;;
\FILE12BUAG-GOLDMINE$;\SERVER24DFSSHAREDCANAGENCYGOLDMINE;/FS3_150a/FILE12/BU/AGENCY/GOLDMINE;90000bytes;98834;;;
\FILE12BUGB-BUSINTEG$;\SERVER24DFSSHAREDCANGBBUSINTEG;/FS3_150a/FILE12/BU/GB/BUSINTEG;50000bytes;988822;;;
\FILE12BUGB-BUSINTEG$;\SERVER24DFSSHAREDCANGBBUSINTEG;/FS3_150a/FILE12/BU/GB/BUSINTEG;50000bytes;988822;other stuff;;

\FILE04BUET-PCO;\SERVER24DFSSHAREDCORPETPROJECT CONTROL OFFICE;/FS7_150a/FILE04/BU-D/PROJECT CONTROL OFFICE;10000bytes;9888;;;
\FILE12BUAG-GOLDMINE$;\SERVER24DFSSHAREDCANAGENCYGOLDMINE;/FS3_150a/FILE12/BU/AGENCY/GOLDMINE;90000bytes;98834;;;
\FILE12BUGB-BUSINTEG$;\SERVER24DFSSHAREDCANGBBUSINTEG;/FS3_150a/FILE12/BU/GB/BUSINTEG;50000bytes;988822;;;Same Physical Path as Line #4
\FILE12BUGB-BUSINTEG$;\SERVER24DFSSHAREDCANGBBUSINTEG;/FS3_150a/FILE12/BU/GB/BUSINTEG;50000bytes;988822;other stuff;; Same Physical Path as Line #3

awk -f script.awk file.txt{,}

BEGIN {
    FS = ";"
}

FNR==NR {
    array[$3]=array[$3] "#" NR
    next
}

{
    if ($3 in array && array[$3] ~ /#.#/) {
        copy = array[$3]
        sub("#"FNR, "", copy)
        printf "%s Same Physical Path as Line as %sn", $0, copy
    }
    else {
        print
    }
}

\FILE04BUET-PCO;\SERVER24DFSSHAREDCORPETPROJECT CONTROL OFFICE;/FS7_150a/FILE04/BU-D/PROJECT CONTROL OFFICE;10000bytes;9888;;;
\FILE12BUAG-GOLDMINE$;\SERVER24DFSSHAREDCANAGENCYGOLDMINE;/FS3_150a/FILE12/BU/AGENCY/GOLDMINE;90000bytes;98834;;;
\FILE12BUGB-BUSINTEG$;\SERVER24DFSSHAREDCANGBBUSINTEG;/FS3_150a/FILE12/BU/GB/BUSINTEG;50000bytes;988822;;; Same Physical Path as Line as #4
\FILE12BUGB-BUSINTEG$;\SERVER24DFSSHAREDCANGBBUSINTEG;/FS3_150a/FILE12/BU/GB/BUSINTEG;50000bytes;988822;other stuff;; Same Physical Path as Line as #3

awk -F';' '{ tag = ""
             if (field3[$3] != 0) tag = " Same physical path as line " field3[$3]
             else field3[$3] = NR
             printf "%s%sn", $0, tag
           }' "$@"

\FILE04BUET-PCO;\SERVER24DFSSHAREDCORPETPROJECT CONTROL OFFICE;/FS7_150a/FILE04/BU-D/PROJECT CONTROL OFFICE;10000bytes;9888;;;
\FILE12BUAG-GOLDMINE$;\SERVER24DFSSHAREDCANAGENCYGOLDMINE;/FS3_150a/FILE12/BU/AGENCY/GOLDMINE;90000bytes;98834;;;
\FILE12BUGB-BUSINTEG$;\SERVER24DFSSHAREDCANGBBUSINTEG;/FS3_150a/FILE12/BU/GB/BUSINTEG;50000bytes;988822;;;
\FILE12BUGB-BUSINTEG$;\SERVER24DFSSHAREDCANGBBUSINTEG;/FS3_150a/FILE12/BU/GB/BUSINTEG;50000bytes;988822;other stuff;; Same physical path as line 3