I can't reproduce this - here's what I did:
PxPlus-2019 Web (Ver:16.10/UNIX-Linux-RedHat) Serno:1610-664-0xxxxxx
(c) Copyright 2005-2018 PVX Plus Technologies Ltd. (All rights reserved)
Website:
http://www.pvxplus.com->010 BEGIN
-:0020 LET BASE64_FILE$="/tmp/50_09790301_13_200_002_led_kalender.base64"
-:0030 LET PDFFIL$="/tmp/50_09790301_13_200_002_led_kalender.pdf"
-:0040 OPEN (1)"*PDF*;FILE="+PDFFIL$+";OVERWRITE"; LIST (1); CLOSE (1)
-:0050 ERASE BASE64_FILE$,ERR=*NEXT
-:0060 CALL "*web/base64;ENCODE_FILE",PDFFIL$,BASE64_FILE$
-:run .
-:open input(1)base64_file$;print rcd(1)
JVBERi0xLjMKJbe+raoKMSAwIG9iago8PAovVHlwZSAvQ2F0YWxvZwovUGFnZXMgMiAwIFIKPj4KZW5kb2JqCjIgMCBvYmoKPDwKL1R5cGUgL1BhZ2VzCi9LaWRzIFsgNSAwIFIgXQovQ291bnQgMQo+PgplbmRvYmoKMyAwIG9iago8PAovUHJvZHVjZXIgKHd3dy5wdnhwbHVzLmNvbSkKL0F1dGhvciAocm9vdCkKL0NyZWF0b3IgKFB4UGx1cy0xNi4xMC4wMDAwKQovVGl0bGUgKFVudGl0bGVkKQovU3ViamVjdCAoTm8gU3ViamVjdCkKL0tleXdvcmRzIChub25lKQovQ3JlYXRpb25EYXRlIChEOjIwMjIwODI0
-:
I open the base64 file in gedit, copy the contents and paste them on that website. The result is the attached picture (the correct PDF contents).