Change Name of a sequence by adding a number for duplicate

I actually have a dataframe such:

old_name       new_name      pident       length
gene1_0035_0042            geneA         100          560
gene2_0035_0042            geneA         100          545
gene3_0042_0035            geneB         99           356
gene4_0042_0035            geneB         97           256
gene6_0035_0042            geneB         96           567

and here is the fasta file (example):

>gene1_0035_0042
ATTGAC
>gene2_0035_0042 
ATGAGCC
>gene3_0042_0035
AGCCAG
>gene4_0042_0035
AGCCAT
>gene6_0035_0042
AGCCATG

in fact I wrote a script to replace in a fasta file the old_name of the sequence by the new_name by doing: (qseqid = old_name and Busco_ID = new_names in the ex).

blast=pd.read_table("matches_Busco_0035_0042_best_hit.m8",header=None)
blast.columns = ["qseqid", "Busco_ID", "pident", "length", "mismatch", "gapopen","qstart", "qend", "sstart", "send", "evalue", "bitscore"]

repl = blast[blast.pident > 95]

repl.to_csv("busco_blast_non-rename.txt",sep='t')

qseqid=repl.ix[:,0]
Busco_ID=repl.ix[:,1]

newfile = []
count = 0
running_inds = {}

for rec in SeqIO.parse("concatenate_0035_0042_dna2.fa", "fasta"):
    #get corresponding value for record ID from dataframe
    #repl["seq"] and "newseq" are the pandas column with the old and new sequence names, respectively
    x = repl.loc[repl["qseqid"] == rec.id, "Busco_ID"]
    #change record, if not empty
    if x.any():
        #append old identifier number to the new id name
        running = running_inds.get(x.iloc[0], 1) # Get the running index for this sequence
        running_inds[x.iloc[0]] = running + 1
        rec.name = rec.description = rec.id = x.iloc[0] + rec.id[rec.id.index("_"):]
        count += 1
    #append record to list
    newfile.append(rec)

#write list into new fasta file
SeqIO.write(newfile, "concatenate_with_busco_names_0035_0042_dna.fa", "fasta")
#tell us, how hard you had to work for us
print("I changed {} entries!".format(count))

as you can see I only filter my sequence by keeping these with a pident > 95 but as you can see I will get for all these sequences the same name which is the new_name but instead of that, I would like to add a number at the end of the new name. For the above example it would give in the fasta file:

>geneA_0035_0042_1
ATTGAC
>geneA_0035_0042_2
ATGAGCC
>geneB_0042_0035_1
AGCCAG
>geneB_0042_0035_2
AGCCAT
>geneB_0035_0042_1
AGCCATG

and so on
instead of:

>geneA_0035_0042
ATTGAC
>geneA_0035_0042
ATGAGCC
>geneB_0042_0035
AGCCAG
>geneB_0042_0035
AGCCAT
>geneB_0035_0042
AGCCATG

as my script does

Thanks for your help

Issue:

I got:

>EOG090X0FA0_0042_0042_1
>EOG090X0FA0_0042_0035_2
>EOG090X0FA0_0035_0035_3
>EOG090X0FA0_0035_0042_4

but since they are all different I should get:

>EOG090X0FA0_0042_0042_1
>EOG090X0FA0_0042_0035_1
>EOG090X0FA0_0035_0035_1
>EOG090X0FA0_0035_0042_1