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I have been in the UK since September 2010. First as a PhD student on tier-4 visa, till 2017 September, then I switched to tier 2 visa from 2017 September till now. I have always had a leave to remain throughout the ten years, but I have been to my home country for vacation multiple times. I also have visited 5 conferences in USA, and been on tourist visits to Europe five times.

I was never out for 6 months at a stretch, but the eligibility for long residence allows only 540 days out of the country in the ten year period - does that mean without leave to remain, or regardless? To see if I qualify, do I need to manually calculate every single time I went out of the country, and add up all the days to see if they are less than 540? Is this how the Home Office calculates this? Any concession for PhD conference travel? Also should I wait for 5 years
on tier-2 if I am ineligible via this route?

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...The eligibility for long residence allows only 540 days out of the country in the ten year period - does that mean without leave to remain, or regardless?

If I understand you correctly, your scenario is covered. That is, you have a valid visa - you leave the country before that expires - it perhaps expires while you are out of country - you acquire another visa, and return to the country (approval within 90 days of expiration of the previous visa).

To see if I qualify, do I need to manually calculate every single time I went out of the country, and add up all the days to see if they are less than 540? Is this how the Home Office calculates this?

Yes and yes. Note that any amount of time during the calender day counts towards being in the country. So even if you boarded a flight that left at 12:30 am, you would count the full day with only 30 minutes of that day as being inside the UK, not out.

Any concession for PhD conference travel?

Nope. But they will scrutinize your time in your home country more closely if you are marginally close (or even slightly over) that 540 limit. There is some discretion for family emergencies, but that's hard to get, and rarely obtained.

Also should I wait for 5 years on tier-2 if I am ineligible via this route?

This is more of an personal preference than a fact, but if it was me (and assuming all eligibility requirements were met), I would have applied back in August when you first qualified 28 days before reaching the ten year mark. If you're application is indeed as 'straightforward' as you portray it, you probably would have already gotten approval and be free of visa restrictions.

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