This concern seems legitimate to me. There is often important information in negative feelings which I mostly explore with Focusing or Internal Family Systems. When my brain thinks that there is still information in that feeling but I am nevertheless applying the HEAL method, it can feel as if I am convincing myself or, as you said, repressing your emotion. That seems indeed somewhat tricky to me. 

However, I also think that there is not always useful information in negative feelings. I often had times where I already explored the negative feeling or knew where it came from but it still came back. Before having heard of HEAL and reading Rick Hanson's material I thought that you always had to fully experience and feel a negative feeling in order to overcome it. I no longer think this is the case, instead I replace it with thoughts or behaviors that are more helpful and in these behaviors also incorporate the useful bits of what the negative feeling tries to achieve. 

I have used it quite a fair bit when I was working full-time on my mental health during a retreat.

I sometimes have resistance to using it. Mostly, when the negative belief that I wanted to counteract was pretty big, exploring the underlying issue using focusing, Internal Family Systems therapy, or some other introspective technique seems more useful in that situation.