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Assuming you've taken the old insoles out if your new ones are particularly thick they may cause you the same fit issues in all other shoes. Different shoes will have different heel shapes but will likely all have insoles similar in thickness to each other as they're fairly standard. What insoles are you using? I've tinkered with insoles in the past for fit but some are easier than others to do this with. Otherwise looking into low profile versions as @cookiemonster suggested may be your best option
I have a question about insoles. I’ve bought some they’ve helped with my ankle issue as well lots of strength training. My issue is that because my foot is raised slightly in the trainer my heel isn’t sitting properly in the ankle box. The issue is all trainers are different so has choosing new trainers just become harder or can I bastardise these insoles to be lower in the heel area