In using flatten:flatten I have found a change in behaviour between 1.3.0 and 1.6.0. Specifically I think that the change is in 1.4.0 as this is the first version at which it fails.
When using flattenDependencyMode=all the plugin seems to try and resolve dependencies parents and now fail if they cannot be fully resolved.

This is reproduced in the simple example project pom attached by calling mvn flatten:flatten
pom.xml.txt

The problem as I understand it is that we have a dependency chain:
com.querydsl:querydsl-core:4.3.1
-> com.infradna.tool:bridge-method-annotation:jar:1.13
-> exclusion: org.jenkins-ci:annotation-indexer:jar:1.4

but that org.jenkins-ci:annotation-indexer:jar:1.4 references an unpublished parent project org.jenkins-ci:jenkins:pom:1.26 which therefore cannot be resolved.

If there is a way to avoid this parent resolution or suppress the failure then that would be helpful as the behaviour at 1.3.0 of flatten-maven-plugin seemed to be sufficient in this use-case.