<?php
$yourinput = "blah
# [[[@-100] Start of custom routes
text content here I cant be sure what it is
# End of custom routes [@-100]]]
more stuff";
$replaced = preg_replace('~(?s)# \[\[\[@-100\] Start of custom routes.*?# End of custom routes \[@-100\]\]\]~', '', $yourinput);
echo $replaced;
PD9waHAKCiR5b3VyaW5wdXQgPSAiYmxhaAojIFtbW0AtMTAwXSBTdGFydCBvZiBjdXN0b20gcm91dGVzCgogICB0ZXh0IGNvbnRlbnQgaGVyZSBJIGNhbnQgYmUgc3VyZSB3aGF0IGl0IGlzCgojIEVuZCBvZiBjdXN0b20gcm91dGVzIFtALTEwMF1dXQptb3JlIHN0dWZmIjsKJHJlcGxhY2VkID0gcHJlZ19yZXBsYWNlKCd+KD9zKSMgXFtcW1xbQC0xMDBcXSBTdGFydCBvZiBjdXN0b20gcm91dGVzLio/IyBFbmQgb2YgY3VzdG9tIHJvdXRlcyBcW0AtMTAwXF1cXVxdficsCiAgICAgICAgICAgICAgICAgICAgICAgICAnJywgJHlvdXJpbnB1dCk7CmVjaG8gJHJlcGxhY2VkOyAgICAgICAgICAgICAgICAgICAgICAgICA=