100% Black Barcodes in Photoshop?

Other methods include:

• In a copy of the grayscale mode barcode file, select all and copy the original channel data. Convert to CMYK. Delete all data out of the CMY channels. In the K channel, paste in the original grayscale data. 
• In a copy of the grayscale mode file, convert to multichannel mode. Add 3 new white channels and move them above the barcode channel so that it is position #4. Image > Mode > CMYK to return the 4 channels as they are (don't use the more common Convert to Profile command in this use case)

Then you can select all and copy and paste the CMYK barcode into the main CMYK file. If you receive any colour management popups, select the option to preserve the numbers/values and not the appearance.

Here is an example of a layered CMYK mode file, where I have used a Clipped Adjustment Layer with the Channel Mixer set to Monochrome mode, to create a black-only channel barcode from the original four channel values. I only needed to mix it to 102% to create solid black, although the screenshot is at 200%.

I don't think that the problem is with your legacy Custom CMYK settings if it has 100% black and Maximum GCR settings.

You can convert to CMYK without flattening, just uncheck the flatten image box... But if some layers use unsupported blend modes then you may get unexpected results in other layers.

The problem with using the legacy Custom CMYK with Maximum GCR is:

* Custom CMYK is not based off any modern printing condition, so it may not be the best choice

* You only want the barcode to be 100K, the rest of the image may not benefit from the same profile conversion

This of course presumes that there is other image content... If all you have is a barcode and nothing else, then all is good!

There are multiple ways to create a 0cmy100k barcode image if that is all you need, with no other content, without having to use Custom CMYK Maximum GCR settings.

Can you post an image to clarify the type of content being converted?

P.S. If all you have is a raster barcode, they are generally best being generated at 100% size at a high resolution and being saved in bitmap mode for use in layout or illustration software. Vector barcodes are preferred over raster.