Switching both clashing functions ( wakeUp1(), wakeUp2() ) to static functions seems to fix linking for me.

This sees to be deadend as there come more function name clashes, and i suspect linking problems come from magic done by arduino IDE.

Current hack for me is include in arduino sketch my lib headers after including MySensors:

#include <MySensors.h>
#include <MyLib.h>

and than inside library use only:

#include <core/MySensorsCore.h>

not sure if its right solution, if one has any better please share.

diff --git a/hal/architecture/AVR/MyHwAVR.cpp b/hal/architecture/AVR/MyHwAVR.cpp
index 5a17b063..a018ab35 100644
--- a/hal/architecture/AVR/MyHwAVR.cpp
+++ b/hal/architecture/AVR/MyHwAVR.cpp
@@ -41,7 +41,7 @@ volatile uint8_t _wakeUp2Interrupt  =
 
 static uint32_t sleepRemainingMs = 0ul;
 
-void wakeUp1(void)
+void static wakeUp1(void)
 {
        // Disable sleep. When an interrupt occurs after attachInterrupt,
        // but before sleeping the CPU would not wake up.
@@ -53,7 +53,7 @@ void wakeUp1(void)
                _wokeUpByInterrupt = _wakeUp1Interrupt;
        }
 }
-void wakeUp2(void)
+void static wakeUp2(void)
 {
        sleep_disable();
        detachInterrupt(_wakeUp2Interrupt);
diff --git a/hal/architecture/NRF5/MyHwNRF5.cpp b/hal/architecture/NRF5/MyHwNRF5.cpp
index d91a0438..f083a17c 100644
--- a/hal/architecture/NRF5/MyHwNRF5.cpp
+++ b/hal/architecture/NRF5/MyHwNRF5.cpp
@@ -28,11 +28,11 @@ volatile uint8_t _wakeUp1Interrupt =
 volatile uint8_t _wakeUp2Interrupt =
     INVALID_INTERRUPT_NUM; // Interrupt number for wakeUp2-callback.
 
-void wakeUp1(void) // place to send the interrupts
+void static wakeUp1(void) // place to send the interrupts
 {
        _wokeUpByInterrupt = _wakeUp1Interrupt;
 }
-void wakeUp2(void) // place to send the second interrupts
+void static wakeUp2(void) // place to send the second interrupts
 {
        _wokeUpByInterrupt = _wakeUp2Interrupt;
 }

#define MY_CORE_ONLY

It solved compiiation errors, but now I have link errors(I have many .cpp/.h files in my lib):

/tmp/arduino_build_899057/libraries/MyLib/Foo.cpp.o (symbol from plugin): In function `wakeUp1()':(.text+0x0): multiple definition of `wakeUp1()'

Seems same as https://forum.mysensors.org/topic/6084/including-mysensors-h-in-multiple-files .
I tried:

#include <core/MySensorsCore.h>

but it fails:

Alternatives for core/MyMessage.h: []In file included from mytest.ino:13:0:
ResolveLibrary(core/MyMessage.h)
  -> candidates: []

MyLib/MyLib.h:10:10: fatal error: core/MyMessage.h: No such file or directory
 #include <core/MyMessage.h>
          ^~~~~~~~~~~~~~~~~~
compilation terminated.

#define MY_CORE_ONLY
#include <MySensors.h>
MyMessage MyVar;

void setup() {}
void loop() {}