Due to dialog with everyone I have come to a firm decision on what to do with those skills you gained during your background generation. I want the skill ranks you put into the Heroes of Legend skills to count but I don't want to take away your choice when it comes to selecting your class skills.
So, with this in mind I present the following rule:
[CLASSRACE]Heroes of Legend: Conversion to D&D 4th Edition[/CLASSRACE][FLAVOR]If you gain skills during your background generation (everyone should have some sort of Survival unless they got knocked down to 0 or less ranks) you will add the converted skill to your class skill list before selecting your trained skills. If you have 6 or more skill ranks in one or more of those skills, you gain a +2 background bonus to those skills. Even if you are not trained in a skill that has 6 or more ranks in it, you still gain the +2 background bonus for having 6+ ranks in that skill.[/FLAVOR]
I believe this ruling is more in line with the standard D&D 4e background rules. I initially was thinking about patterning this after the Heroes of the Feywild character background generation chapter, but Heroes of Legend is actually more restrictive in the skill section than the HotF material.
Now you may choose whatever skills you want to be trained in, possibly be lucky to gain bonuses in some untrained skills due to your experiences. AND you won't lose any of your trained skills to chance.