Ok, to hide the popup, you need to comment out line 130 in FrontentBar.cpp file (PresetHandler::showMessageWindow("Sample Folder changed).
The "The sample directory does not exist" text can be changed by editing line 197 in ModulatorSamplerData.cpp (the one below "sampler->getMainController()->sendOverlayMessage(DeactiveOverlay::State::CustomErrorMessage,").
Hope this helps somebody! :-)