Word frequencies from large body of scraped text
for i in range(1 ,num_batches +1):


Your inter-token spacing here is a little wonky. I suggest running this code through a linter to get it to be PEP8-compliant.

This string:

r'input_batch_' + str(i) + r'.txt'


can be:

f'input_batch_{i}.txt'


This code:

entries_raw = infile.readlines()
entries_single = [x.strip() for x in entries_raw]
entries = [x.split('\t') for x in entries_single]


can also be simplified, to:

entries = [line.rstrip().split('\t') for line in infile]


Note a few things. You don't need to call readlines(); you can treat the file object itself as an iterator. Also, avoid calling a variable x even if it's an intermediate variable; you need meaningful names.

This is an antipattern inherited from C:

for j in range(len(entries)):
    data.loc[j] = entries[j][1], entries[j][0]


You should instead do:

for j, entry in enumerate(entries):
    data.loc[j] = entry[1], entry[0]


That also applies to your for x in range(len(data)):.

This:

freq_dict = dict()


should be:

freq_dict = {}


This:

if key in freq_dict:
    prior_freq = freq_dict.get(key)
    freq_dict[key] = prior_freq + data['freq'][x]
else:
    freq_dict[key] = data['freq'][x]


can be simplified to:

prior_freq = freq_dict.get(key)
freq_dict[key] = data['freq'][x]
if prior_freq is not None:
    freq_dict[key] += prior_freq


or even (courtesy @AlexHall):

freq_dict[key] = data['freq'][x] + freq_dict.get(key, 0)


Note a few things. First of all, you were inappropriately using get - either check for key presence and then use [], or use get and then check the return value (which is preferred, as it requires fewer key lookups).

This loop:

for key in freq_dict.keys():
outfile.write("%s,%s\n" % (key, freq_dict[key]))


needs adjustment in a few ways. Firstly, it won't run at all because its indentation is wrong. Also, rather that only iterating over keys, you should be iterating over items:

for key, freq in freq_dict.items():
    outfile.write(f'{key},{freq}\n')