diff --git a/api/src/org/labkey/api/pipeline/PipelineJob.java b/api/src/org/labkey/api/pipeline/PipelineJob.java
index 055699b030f..18e595703a3 100644
--- a/api/src/org/labkey/api/pipeline/PipelineJob.java
+++ b/api/src/org/labkey/api/pipeline/PipelineJob.java
@@ -473,16 +473,17 @@ public Path getRemoteLogPath()
     /** Finds a file name that hasn't been used yet, appending ".2", ".3", etc as needed */
     public static File findUniqueLogFile(File primaryFile, String baseName)
     {
+        String validBaseName = FileUtil.makeLegalName(baseName);
         // need to look in current and archived dirs for any unused log file names (issue 20987)
-        File fileLog = FT_LOG.newFile(primaryFile.getParentFile(), baseName);
+        File fileLog = FT_LOG.newFile(primaryFile.getParentFile(), validBaseName);
         File archivedDir = new File(primaryFile.getParentFile(), AssayFileWriter.ARCHIVED_DIR_NAME);
-        File fileLogArchived = FT_LOG.newFile(archivedDir, baseName);
+        File fileLogArchived = FT_LOG.newFile(archivedDir, validBaseName);
 
         int index = 1;
         while (NetworkDrive.exists(fileLog) || NetworkDrive.exists(fileLogArchived))
         {
-            fileLog = FT_LOG.newFile(primaryFile.getParentFile(), baseName + "." + (index));
-            fileLogArchived = FT_LOG.newFile(archivedDir, baseName + "." + (index++));
+            fileLog = FT_LOG.newFile(primaryFile.getParentFile(), validBaseName + "." + (index));
+            fileLogArchived = FT_LOG.newFile(archivedDir, validBaseName + "." + (index++));
         }
 
         return fileLog;
diff --git a/api/src/org/labkey/api/util/FileType.java b/api/src/org/labkey/api/util/FileType.java
index 80d274fa6f7..680795aafaa 100644
--- a/api/src/org/labkey/api/util/FileType.java
+++ b/api/src/org/labkey/api/util/FileType.java
@@ -243,7 +243,9 @@ public FileType(List<String> suffixes, String defaultSuffix, boolean dir, gzSupp
     private String tryName(Path parentDir, String name)
     {
         if (_supportGZ.booleanValue())  // TPP treats xml.gz as a native format
-        {   // in the case of existing files, non-gz copy wins if present
+        {
+            FileUtil.legalPathPartThrow(name);
+            // in the case of existing files, non-gz copy wins if present
             Path f = parentDir!=null ? FileUtil.appendName(parentDir, name) : Path.of(name);
             if (!NetworkDrive.exists(f))
             {  // non-gz copy doesn't exist - how about .gz version?
@@ -340,7 +342,7 @@ public String getName(Path parentDir, String basename)
             for (String suffix : _suffixes)
             {
                 String name = tryName(parentDir, basename + suffix);
-                Path f = parentDir.resolve(name);
+                Path f = FileUtil.appendName(parentDir, name);
                 if (NetworkDrive.exists(f))
                 {
                     // avoid, for example, mistaking protxml ".pep-prot.xml" for pepxml ".xml" file
@@ -372,7 +374,7 @@ public File getFile(File parentDir, String basename)
 
     public Path getPath(Path parentDir, String basename)
     {
-        return parentDir.resolve(getName(parentDir, basename));
+        return FileUtil.appendName(parentDir, getName(parentDir, basename));
     }
 
     /**
diff --git a/api/src/org/labkey/api/util/FileUtil.java b/api/src/org/labkey/api/util/FileUtil.java
index a2ac2bc5b68..e56a9b50827 100644
--- a/api/src/org/labkey/api/util/FileUtil.java
+++ b/api/src/org/labkey/api/util/FileUtil.java
@@ -890,7 +890,7 @@ public static Path appendName(Path dir, String name)
 
     // narrower check than isLegalName() or isAllowedFileName()
     // this check that a name is a valid path part (e.g. filename) and is not path like.
-    private static void legalPathPartThrow(String name)
+    public static void legalPathPartThrow(String name)
     {
         int invalidCharacterIndex = StringUtils.indexOfAny(name, '/', File.separatorChar);
         if (invalidCharacterIndex >= 0)