In your first block, open file in binary write mode (wb), since you are writing binary to it. Also, you don't need to convert it explicitly to str. It should look like this:

file = open('code.txt', 'wb')
for line in open('somefile.pdf', 'rb').readlines():
    file.write(line)
file.close()

For second block, open file in read binary mode (rb). Here also, no need to explicitly convert to bytes. It should look like this:

file = open('new.pdf', 'wb')
for line in open('code.txt', 'rb').readlines():
    file.write(line)
file.close()

This should do the trick. But why do you need to convert it in the first place? Keeping file intact will save your hardwork and computational power.

It's not surprising that this is too slow: you're reading data byte-by-byte. For faster performance you would need to read larger buffers at a time.

If you want to compare files by content, use the filecmp package.

There are also some glaring problems with this code. For example, instead of opening a file, doing something in a try block and closing the file handle manually, you should use the recommended with-resources technique:

    with open(filename1, "rb") as f:
        b = f.read(1)
        # ...

Finally, the function name and all variable names are very poor, and don't help the readers understand their purpose and what you're trying to do.

import requests
import io
from PIL import Image

url = 'https://www.gati.com/viewPOD2.jsp?dktno=322012982'
r = requests.get(url)

pil_bytes = io.BytesIO(r.content)
pil_image = Image.open(pil_bytes)

# Needed to get around ValueError: cannot save mode RGBA
rgb = Image.new('RGB', pil_image.size)
rgb.paste(pil_image)
rgb.save('downloaded_image.pdf', 'PDF')

In such cases, it's preferred to send file data passing that with the files keyword, like so:

import requests


def send_pdf_data(filename_list, encoded_pdf_data):
    files = {}

    for (filename, encoded, index) in zip(filename_list, encoded_pdf_data, range(len(filename_list))):
        files[f"pdf_name_[index].pdf"] = (filename, open(filename, 'rb'), 'application/pdf')

    data = {}
    # *Put whatever you want in data dict*

    requests.post("http://yourserveradders", data=data, files=files)


def main():
    filename_list = ["pdf_name_1.pdf", "pdf_name_2.pdf"]
    pdf_blob_data = [open(filename, 'wb').read() for filename
                     in filename_list]

if __name__ == '__main__':
    main()

However, if you really want to pass data as json, you should use base-64 module as @Mark Ransom mentioned.

You can implement it in this way:

import requests
import json
import base64


def encode(data: bytes):
    """
    Return base-64 encoded value of binary data.
    """
    return base64.b64encode(data)


def decode(data: str):
    """
    Return decoded value of a base-64 encoded string.
    """
    return base64.b64decode(data.encode())


def get_pdf_data(filename):
    """
    Open pdf file in binary mode,
    return a string encoded in base-64.
    """
    with open(filename, 'rb') as file:
        return encode(file.read())


def send_pdf_data(filename_list, encoded_pdf_data):
    data = {}
    # *Put whatever you want in data dict*
    # Create content dict.
    content = [dict([("name", filename), ("data", pdf_data)])
               for (filename, data) in zip(filename_list, encoded_pdf_data)]
    data["content"] = content

    data = json.dumps(data) # Convert it to json.
    requests.post("http://yourserveradders", data=data)


def main():
    filename_list = ["pdf_name_1.pdf", "pdf_name_2.pdf"]
    pdf_blob_data = [get_pdf_data(filename) for filename
                     in filename_list]

if __name__ == '__main__':
    main()