Waldbaer

Also, you don't have to move the master layer on each spread individually.
You can select the master layer on one document page, right-click, and choose Edit Linked. Then you can use the menu item Layer > Arrange > Move to Front. Then click on the Finish button.
That will move the master layer to the top of the layer stack on all the spreads.
Of course, that is a one-time action, so if you draw anything on a page after that, you need to ensure it gets inserted below the master layer. Or you need to do that layer arrangement at the end of the project.
Also, in case it's not obvious, you can have multiple Master Pages applied to a single document page, so just put your "Draft" text on a separate Master, to facilitate this kind of layer arrangement.

Trying out would work nicely as a work flow if the batch dialogue's settings were saved, so you'd only have to set the new input files to finally run the batch. As this is not the case, you have to repeat all settings which not only takes time but also provokes errors. So yes, different destination is always to be recommended, but the workflow gets not really better including testing of each batch operation, I think.

Thank you for taking the time to do that, it's much appreciated.
It certainly does appear to be this app, I'll be downloading a trial version to test on my machine and I'll use your screen recordings to log this issue with our devs, although I can't guarantee future compatibility as I'm not certain how the Default Folder X software directly affects handling of path data, and whether this is something that can be changed to be compatible with Affinity.
I understand the frustration, for the time being I'd recommend closing the app whilst running batch jobs, and if I receive any update from our developers I'll be sure to post it here!

Thank you again for checking this out! The interesting thing for me is still that it works sometimes and sometimes not and the path is always entered into the dialogue. I'll send this thread to stclairsoft, too; as far as I experienced, they have a really nice and responsive customer support, too, and this is really the first time I have an issue with it although I'm using its enhanced dialogues nearly all the time and everywhere.

If it's any consolation I recall seeing similar behaviour ( some time ago) to what you are seeing with some files not being processed by the batch function
I abandoned my efforts in Affinity and used FastStone instead to do all my batch processing work.
Cant suggest a way to recreate what I experienced (too long ago) but if you can come up with a recreatable scenario that the Devs can reproduce they may be able to see what is occurring.
Hang on in there.