Since .persist() is to indicate that the expansion is not provided through eCloud but through a plugin, if this is true, there is no need to check against eCloud entries.

src/main/java/me/clip/placeholderapi/expansion/manager/CloudExpansionManager.java

@@ -220,7 +220,7 @@ public final class CloudExpansionManager {
                             plugin.getLocalExpansionManager().findExpansionByName(name);
                         if (localOpt.isPresent()) {
                           PlaceholderExpansion local = localOpt.get();
-                          if (local.isRegistered()) {
+                          if (local.isRegistered() && !local.persist()) {
                             expansion.setHasExpansion(true);
                             expansion.setShouldUpdate(
                                 !local.getVersion().equalsIgnoreCase(expansion.getLatestVersion()));