diff --git a/flow/src/org/labkey/flow/controllers/executescript/AnalysisScriptController.java b/flow/src/org/labkey/flow/controllers/executescript/AnalysisScriptController.java
index 1b2ebe2cc..ca8a27838 100644
--- a/flow/src/org/labkey/flow/controllers/executescript/AnalysisScriptController.java
+++ b/flow/src/org/labkey/flow/controllers/executescript/AnalysisScriptController.java
@@ -54,6 +54,7 @@
 import org.labkey.api.view.HttpView;
 import org.labkey.api.view.JspView;
 import org.labkey.api.view.NavTree;
+import org.labkey.api.view.NotFoundException;
 import org.labkey.api.view.RedirectException;
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.api.view.template.PageConfig;
@@ -95,6 +96,7 @@
 import java.io.IOException;
 import java.net.URI;
 import java.nio.file.Files;
+import java.nio.file.InvalidPathException;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -370,8 +372,15 @@ protected ModelAndView confirmRuns(ImportRunsForm form, BindException errors)
         {
             validatePipeline();
 
-            collectNewPaths(form, errors);
-            return new JspView<PipelinePathForm>("/org/labkey/flow/controllers/executescript/confirmRunsToImport.jsp", form, errors);
+            try
+            {
+                collectNewPaths(form, errors);
+                return new JspView<PipelinePathForm>("/org/labkey/flow/controllers/executescript/confirmRunsToImport.jsp", form, errors);
+            }
+            catch (InvalidPathException e)
+            {
+                throw new NotFoundException(e.getMessage());
+            }
         }
 
         protected ModelAndView uploadRuns(ImportRunsForm form, BindException errors) throws Exception
@@ -985,7 +994,7 @@ private void accelerateWizard(ImportAnalysisForm form, BindException errors, Run
 
             // Set the data folder if we aren't using an existing run
             if (SelectFCSFileOption.None == form.getSelectFCSFilesOption())
-                form.setKeywordDir(new String[]{getWorkspaceFolder(form).toString()});
+                form.setKeywordDir(new String[]{getPipeRoot().relativePath(getWorkspaceFolder(form))});
 
             // Select FCS file (by default we already select all fcs files in working folder)
             stepSelectFCSFiles(form, errors);
diff --git a/luminex/src/org/labkey/luminex/LuminexUploadWizardAction.java b/luminex/src/org/labkey/luminex/LuminexUploadWizardAction.java
index 6bfbcdb24..f529fdbc7 100644
--- a/luminex/src/org/labkey/luminex/LuminexUploadWizardAction.java
+++ b/luminex/src/org/labkey/luminex/LuminexUploadWizardAction.java
@@ -402,8 +402,8 @@ else if (titrationEntry.getValue().isStandard())
             boolean existingSinglePointControl = existingSinglePointControls.contains(singlePointControl);
 
             propertyName = getSinglePointControlCheckboxNameAndId(singlePointControl);
-            // If we have an existing singlePointControl as a baseline from the run we're replacing, use its value
-            defVal = existingSinglePointControl ? "true" : defaultWellRoleValues.get(propertyName);
+            // Issue 54242: If we are in the reRun case, use the existing singlePointControl value as baseline
+            defVal = reRun != null ? (existingSinglePointControl ? "true" : "false") : defaultWellRoleValues.get(propertyName);
             value = setInitialSinglePointControlInput(errorReshow, propertyName, defVal) ? "true" : "";
             view.getDataRegion().addHiddenFormField(propertyName, value);
         }
diff --git a/protein/src/org/labkey/protein/ProteinModule.java b/protein/src/org/labkey/protein/ProteinModule.java
index 310c61ca9..ce0eb2955 100644
--- a/protein/src/org/labkey/protein/ProteinModule.java
+++ b/protein/src/org/labkey/protein/ProteinModule.java
@@ -20,15 +20,15 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
-import org.labkey.api.data.DatabaseMigrationConfiguration;
-import org.labkey.api.data.DatabaseMigrationService;
-import org.labkey.api.data.DatabaseMigrationService.DefaultMigrationSchemaHandler;
 import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.SqlExecutor;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.files.FileContentService;
 import org.labkey.api.files.TableUpdaterFileListener;
+import org.labkey.api.migration.DatabaseMigrationConfiguration;
+import org.labkey.api.migration.DatabaseMigrationService;
+import org.labkey.api.migration.DefaultMigrationSchemaHandler;
 import org.labkey.api.module.DefaultModule;
 import org.labkey.api.module.ModuleContext;
 import org.labkey.api.pipeline.PipelineService;
@@ -153,7 +153,7 @@ public void beforeSchema()
             }
 
             @Override
-            public void afterSchema(DatabaseMigrationConfiguration configuration, DbSchema sourceSchema, DbSchema targetSchema, Map<String, Map<String, Sequence>> sequenceMap)
+            public void afterSchema(DatabaseMigrationConfiguration configuration, DbSchema sourceSchema, DbSchema targetSchema)
             {
                 new SqlExecutor(getSchema()).execute("ALTER TABLE prot.Organisms ADD CONSTRAINT FK_ProtOrganisms_ProtIdentifiers FOREIGN KEY (IdentId) REFERENCES prot.Identifiers (IdentId)");
                 GoLoader.createGoIndexes();