Fix Operation Timestamps in Tests (elastic#43155)

* For the issue in elastic#43086 we were running into inactive shards because the random timestamps previously used would randomly make `org.elasticsearch.index.shard.IndexShard#checkIdle` see an incorrect+huge  inactive time
* Also fixed one other spot in tests that passed `ms` instead of `ns` for the same timestamp on an index op to correctly use relative `ns`
* Closes elastic#43086

server/src/test/java/org/elasticsearch/indices/flush/FlushIT.java

@@ -275,7 +275,7 @@ public void testUnallocatedShardsDoesNotHang() throws InterruptedException {
     private void indexDoc(Engine engine, String id) throws IOException {
         final ParsedDocument doc = InternalEngineTests.createParsedDoc(id, null);
         final Engine.IndexResult indexResult = engine.index(new Engine.Index(new Term("_id", Uid.encodeId(doc.id())), doc,
-            engine.getLocalCheckpoint() + 1, 1L, 1L, null, Engine.Operation.Origin.REPLICA, randomLong(), -1L, false,
+            engine.getLocalCheckpoint() + 1, 1L, 1L, null, Engine.Operation.Origin.REPLICA, System.nanoTime(), -1L, false,
             SequenceNumbers.UNASSIGNED_SEQ_NO, 0));
         assertThat(indexResult.getFailure(), nullValue());
     }

test/framework/src/main/java/org/elasticsearch/index/engine/EngineTestCase.java

@@ -834,7 +834,7 @@ public List<Engine.Operation> generateHistoryOnReplica(int numOps, boolean allow
             final Engine.Operation.TYPE opType = randomFrom(Engine.Operation.TYPE.values());
             final boolean isNestedDoc = includeNestedDocs && opType == Engine.Operation.TYPE.INDEX && randomBoolean();
             final int nestedValues = between(0, 3);
-            final long startTime = threadPool.relativeTimeInMillis();
+            final long startTime = threadPool.relativeTimeInNanos();
             final int copies = allowDuplicate && rarely() ? between(2, 4) : 1;
             for (int copy = 0; copy < copies; copy++) {
                 final ParsedDocument doc = isNestedDoc ? nestedParsedDocFactory.apply(id, nestedValues) : createParsedDoc(id, null);