The counters serve the same purpose, we only need to know the count of the actual replies rendered to the view in order to calculate the replyIndex

src/state/queries/usePostThread/traversal.ts

@@ -135,11 +135,11 @@ export function sortAndAnnotateThreadItems(
       } else if (AppBskyUnspeccedDefs.isThreadItemPost(item.value)) {
         if (parentMetadata) {
           /*
-           * Set this value before incrementing the `repliesIndexCounter`, since
-           * `repliesIndexCounter` is 1-indexed and `replyIndex` is 0-indexed.
+           * Set this value before incrementing the `repliesSeenCounter` later
+           * on, since `repliesSeenCounter` is 1-indexed and `replyIndex` is
+           * 0-indexed.
            */
-          metadata!.replyIndex = parentMetadata.repliesIndexCounter
-          parentMetadata.repliesIndexCounter += 1
+          metadata!.replyIndex = parentMetadata.repliesSeenCounter
         }
 
         const post = views.threadPost({
@@ -194,12 +194,11 @@ export function sortAndAnnotateThreadItems(
                 if (childParentMetadata) {
                   /*
                    * Set this value before incrementing the
-                   * `repliesIndexCounter`, since `repliesIndexCounter` is
-                   * 1-indexed and `replyIndex` is 0-indexed.
+                   * `repliesSeenCounter` later on, since `repliesSeenCounter`
+                   * is 1-indexed and `replyIndex` is 0-indexed.
                    */
                   childMetadata!.replyIndex =
-                    childParentMetadata.repliesIndexCounter
-                  childParentMetadata.repliesIndexCounter += 1
+                    childParentMetadata.repliesSeenCounter
                 }
 
                 const childPost = views.threadPost({

src/state/queries/usePostThread/types.ts

@@ -193,13 +193,14 @@ export type TraversalMetadata = {
    */
   repliesUnhydrated: number
   /**
-   * The number of replies that have been seen so far in the traversal.
-   * Excludes replies that are moderated in some way, since those are not
-   * "seen" on first load. Use `repliesIndexCounter` for the total number of
-   * replies that were hydrated in the response.
+   * The number of replies that have been "seen" (actually able to be rendered)
+   * so far in the traversal. Excludes replies that are moderated in some way,
+   * since those are not "seen" on first load.
    *
-   * After traversal, we can use this to calculate if we actually got all the
-   * replies we expected, or if some were blocked, etc.
+   * We use this to compute the `replyIndex` values of the children of this
+   * parent. E.g. if a reply is not hydrated on the response, or is moderated
+   * in some way (including by the user), this value is not incremented. So
+   * this represents the _actual_ index of the reply in the rendered view.
    *
    * Note: this is a "counter", not an "index". Because this value is
    * incremented starting from 0, it is 1-indexed. So to when comparing to the
@@ -207,17 +208,9 @@ export type TraversalMetadata = {
    */
   repliesSeenCounter: number
   /**
-   * The total number of replies to this post hydrated in this response. Used
-   * for populating the `replyIndex` of the post by referencing this value on
-   * the parent.
-   *
-   * Note: this is a "counter", not an "index". Because this value is
-   * incremented starting from 0, it is 1-indexed. So to when comparing to the
-   * `replyIndex`, you'll need to subtract 1 from this value.
-   */
-  repliesIndexCounter: number
-  /**
-   * The index-0-based index of this reply in the parent post's replies.
+   * The index-0-based index of this reply in the parent post's replies. This
+   * is computed from the `repliesSeenCounter` of the parent post, prior to it
+   * being incremented for this reply.
    */
   replyIndex: number
   /**

src/state/queries/usePostThread/utils.ts

@@ -99,7 +99,6 @@ export function getTraversalMetadata({
     repliesCount,
     repliesUnhydrated,
     repliesSeenCounter: 0,
-    repliesIndexCounter: 0,
     replyIndex: 0,
     skippedIndentIndices: new Set<number>(),
   }