fb2kPortable add foobar2000\encoders to DirectoriesToPreserve in installer.ini
The official encoder pack installs to foobar2000\encoders; amending installer.ini with
PreserveDirectory3=App\foobar2000\encoders
would make user installed encoders persist fb2kPortable upgrades.
Also, foobar2000\components are foobar2000 shipped component dlls, that are rebuilt with every release and should probably not be preserved; user components as of v2.x reside in profile\user-components{,-x64}.