BR tags with class replaced with nbsp

I created editor like this:

CKEDITOR.replace( 'editor1', {
    extraAllowedContent: 'br(*)'
} );

And editor correctly preserved:

<p>foo<br class="bom" />
bar</p>

Are you sure that you cleared cache after changing config.js file?

Although, after a while I thought that you might want to use <br> at the end of block. Such <br>s have special meaning in contenteditable elements and you simply cannot use them. But first of all, you should not use CKEditor to edit a layout which needs clear fix hacks. Read more in CKEditor - basic concepts.

Not sure if you managed, it but I spent all night fixing this.
Very, very aggravating issue.
Syntactically it makes sense that some <br> are removed, but the ones with styles or classes applied should always be left alone.

To correct the issue - at least in part, some are still being removed despite the class, Download this file:
http://dev.ckeditor.com/browser/CKEditor/trunk/_source/plugins/htmldataprocessor/plugin.js

Create the plugin folder in the same path, then include the plugin in your configuration file:
config.extraPlugins = 'htmldataprocessor';

This is likely unrelated, but I also have the following in the settings:

config.enterMode = CKEDITOR.ENTER_BR;
config.shiftEnterMode = CKEDITOR.ENTER_P;
config.allowedContent = true; // don't filter my data
extraAllowedContent: 'br(*)';

And the phraser that sets the code formatting options to keep my sources somewhat readable:

CKEDITOR.on('instanceReady', function( ev ) {
    //Set the write instance
    var writer = ev.editor.dataProcessor.writer;
    // The character sequence to use for every indentation step.
    writer.indentationChars = '\t';
    // The way to close self closing tags, like <br />.
    writer.selfClosingEnd = ' />';
    // The character sequence to be used for line breaks.
    writer.lineBreakChars = '\n';
    // The writing rules for <div> tag.
    writer.setRules( 'div',
        {
            // Indicates that this tag causes indentation on line breaks inside of it.
            indent : true,
            // Inserts a line break before the <p> opening tag.
            breakBeforeOpen : false,
            // Inserts a line break after the <p> opening tag.
            breakAfterOpen : true,
            // Inserts a line break before the </p> closing tag.
            breakBeforeClose : true,
            // Inserts a line break after the </p> closing tag.
            breakAfterClose : true
        });
    var blockTags = ['h1','h2','h3','h4','h5','h6','p','pre','ul','li'];
    var rules = {
    indent : true,
    breakBeforeOpen : true,
    breakAfterOpen : false,
    breakBeforeClose : false,
    breakAfterClose : true
    };
    for (var i=0; i<blockTags.length; i++) {
        writer.setRules( blockTags[i], rules );
    }

});

Again, it's not an actual "fix" that makes it work all the time, but at least it makes it stop replacing most of the breaks that are actually needed.