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Hello, it may be an issue as this is what the government guidance states: If you do not register, your permission to stay might be shortened and you’ll have to leave the UK. You can also be stopped from getting or extending a UK visa in future.
I would advise you to get registered before you make your ILR application and hope that they do not raise this as an issue and they exercise their discretion in your favour.
All the best.
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