Tests not complete yet

src/SIL.Machine/Corpora/UpdateUsfmParserHandler.cs

@@ -378,7 +378,7 @@ private bool ReplaceWithNewTokens(UsfmParserState state)
             bool useNewTokens =
                 _behavior == UpdateUsfmBehavior.StripExisting
                 || (newText && !existingText)
-                || (newText && _behavior == UpdateUsfmBehavior.PreferNew);
+                || (newText && _behavior == UpdateUsfmBehavior.PreferNew && !state.IsReferenceText);
 
             if (useNewTokens)
                 _tokens.AddRange(_newTokens);

src/SIL.Machine/Corpora/UsfmParserState.cs

@@ -76,10 +76,9 @@ public UsfmParserState(UsfmStylesheet stylesheet, ScrVers versification, IReadOn
         /// </summary>
         public int SpecialTokenCount { get; internal set; }
 
-        /// <summary>
-        /// True if the token processed is a figure.
-        /// </summary>
-        public bool IsFigure => CharTag?.Marker == "fig";
+        public bool IsReferenceText =>
+            !(CharTag is null)
+            && (UsfmStylesheet.IsReference(CharTag.Marker) || UsfmStylesheet.IsFigure(CharTag.Marker));
 
         /// <summary>
         /// Current paragraph tag or null for none.

src/SIL.Machine/Corpora/UsfmStylesheet.cs

@@ -11,6 +11,10 @@ namespace SIL.Machine.Corpora
     public class UsfmStylesheet
     {
         private static readonly Regex CellRangeRegex = new Regex(@"^(t[ch][cr]?[1-5])-([2-5])$", RegexOptions.Compiled);
+        private static readonly Regex ReferenceRegex = new Regex(
+            @"^(fl|fr|fv|r|rq|va|vp|xo|xop|xot|xnt|xdc|xt|zpa-x[bcv])$",
+            RegexOptions.Compiled
+        );
 
         private static readonly Dictionary<string, UsfmJustification> JustificationMappings = new Dictionary<
             string,
@@ -111,6 +115,16 @@ public static bool IsCellRange(string tag, out string baseMarker, out int colSpa
             return false;
         }
 
+        public static bool IsReference(string tag)
+        {
+            return !(tag is null) && ReferenceRegex.IsMatch(tag);
+        }
+
+        public static bool IsFigure(string tag)
+        {
+            return tag == "fig";
+        }
+
         private static IEnumerable<string> GetEmbeddedStylesheet(string fileName)
         {
             using (

tests/SIL.Machine.Tests/Corpora/TestData/usfm/Tes/41MATTes.SFM

@@ -22,6 +22,7 @@
 \v 7
 \v 8
 \c 2
+\r (Mark 1:2-3; Luke 4:5-6)
 \tr \tc1 Row one, column one. \tc2 Row one, column two.
 \tr \tc1 Row two, column one. \tc2 Row two, column two.
 \s1 Chapter \it Two \it*
@@ -38,7 +39,7 @@
 \p
 \v 6 Chapter two, verse \w six|strong="12345" \w*.
 \p
-\v 6 Bad verse. \x - \xo abc\xt 123\x* and more content.
+\v 6 Bad verse. \x - \xo 2:3-4 \xt Cool Book 3:24 \xta The annotation \x* and more content.
 \p
 \v 5 Chapter two, verse five \rq (MAT 3:1)\rq*.
 \v 7a Chapter two, verse seven A,

tests/SIL.Machine.Tests/Corpora/UpdateUsfmParserHandlerTests.cs

@@ -76,7 +76,7 @@ public void GetUsfm_Verse_SkipNote()
     }
 
     [Test]
-    public void GetUsfm_Verse_ReplaceNote()
+    public void GetUsfm_Verse_ReplaceNoteKeepReference()
     {
         var rows = new List<(IReadOnlyList<ScriptureRef>, string)>
         {
@@ -87,7 +87,38 @@ public void GetUsfm_Verse_ReplaceNote()
         string target = UpdateUsfm(rows);
         Assert.That(
             target,
-            Contains.Substring("\\v 1 First verse of the second chapter. \\f + \\ft This is a new footnote.\\f*\r\n")
+            Contains.Substring(
+                "\\v 1 First verse of the second chapter. \\f + \\fr 2:1: \\ft This is a new footnote.\\f*\r\n"
+            )
+        );
+    }
+
+    [Test]
+    public void GetUsfm_Verse_PreserveFiguresAndReferences()
+    {
+        var rows = new List<(IReadOnlyList<ScriptureRef>, string)>
+        {
+            // fig
+            (ScrRef("MAT 1:5"), "Fifth verse of the first chapter."),
+            (ScrRef("MAT 1:5/1:fig"), "figure text not updated"),
+            // rq
+            (ScrRef("MAT 2:5/1:rq"), "quote reference not updated"),
+            // r
+            (ScrRef("MAT 2/1:r"), "parallel reference not updated"),
+            // xo
+            (ScrRef("MAT 2:6/3:xo"), "Cross reference not update"),
+            // xt
+            (ScrRef("MAT 2:6/4:xt"), "cross reference - target reference not updated"),
+            // xta
+            (ScrRef("MAT 2:6/5:xta"), "cross reference annotation updated"),
+        };
+
+        string target = UpdateUsfm(rows);
+        Assert.That(
+            target,
+            Contains.Substring(
+                "\\v 1 First verse of the second chapter. \\f + \\fr 2:1: \\ft This is a new footnote.\\f*\r\n"
+            )
         );
     }