[Docs] Clarify caveats for phonetic filters replace option

The `replace` option in the phonetic token filter can have suprising side
effects, e.g. such as described in elastic#26921. This PR adds a note to be mindful
about such scenarios and offers alternatives to using the `replace` option.

Closes elastic#26921

docs/plugins/analysis-phonetic.asciidoc

@@ -65,6 +65,14 @@ GET phonetic_sample/_analyze
 
 <1> Returns: `J`, `joe`, `BLKS`, `bloggs`
 
+It is important to note that `"replace": false` can lead to unexpected behaviour since
+the original and the phonetic version are both kept at the same token location. Some
+queries, e.g. the `match` query with applied fuzzyness, ignore one of these two token
+versions. This can lead to issues that are difficult to diagnose and reason about.
+For this reason, it is often beneficial to use separate fields for analysis with and
+without phonetic filtering. That way searches can be run against both fields with differing
+boosts and trade-offs (e.g. only run fuzzy queries on the original text field, but not the
+phonetic version).
 
 [float]
 ===== Double metaphone settings