Logstash uses SHA1 MessageDigest hashing algorithm to create hash code for comparison.

• logstash/logstash-core/src/main/java/org/logstash/config/ir/PipelineConfig.java

  Line 108 in 8d10baa

  configHash = DigestUtils.sha1Hex(configString() + metadataString());

Switch to SHA256 or other algorithm that has less collision rate.