Index: trunk/ppMerge/src/ppMergeLoop_Threaded.c
===================================================================
--- trunk/ppMerge/src/ppMergeLoop_Threaded.c	(revision 21365)
+++ trunk/ppMerge/src/ppMergeLoop_Threaded.c	(revision 23166)
@@ -137,4 +137,5 @@
     assert(output && output->fpa);
     pmFPA *outFPA = output->fpa;        ///< Output FPA
+    pmHDU *lastHDU = NULL;              // Last HDU that was updated
     int cellNum = 0;                    ///< Index of cell
     if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) {
@@ -156,4 +157,13 @@
                 // No data here
                 continue;
+            }
+
+            // Update the header
+            {
+                pmHDU *hdu = pmHDUGetHighest(outFPA, outChip, outCell); // HDU for file
+                if (hdu && hdu != lastHDU) {
+                    ppMergeVersionHeader(hdu->header);
+                    lastHDU = hdu;
+                }
             }