diff --git a/libraries/AP_HAL/Semaphores.cpp b/libraries/AP_HAL/Semaphores.cpp
index 65890007e2..1ebb9cbe22 100644
--- a/libraries/AP_HAL/Semaphores.cpp
+++ b/libraries/AP_HAL/Semaphores.cpp
@@ -12,14 +12,18 @@ WithSemaphore::WithSemaphore(AP_HAL::Semaphore *mtx, uint32_t line) :
 WithSemaphore::WithSemaphore(AP_HAL::Semaphore &mtx, uint32_t line) :
     _mtx(mtx)
 {
+#ifndef HAL_BOOTLOADER_BUILD
     bool in_main = hal.scheduler->in_main_thread();
     if (in_main) {
         hal.util->persistent_data.semaphore_line = line;
     }
+#endif
     _mtx.take_blocking();
+#ifndef HAL_BOOTLOADER_BUILD
     if (in_main) {
         hal.util->persistent_data.semaphore_line = 0;
     }
+#endif
 }
 
 WithSemaphore::~WithSemaphore()