I agree that you should make a stand, although I won't be quite as much of a firebrand about it as Todd.
Those questions are more than reasonable, complying with HMRC inspections is expensive and stressful and I think it's our professional duty to push back when HMRC attempt to launch multiple investigations into the same client over a short period of time.
At the very least, even if the inspection goes ahead, you will have established your objections from the outset and this can be useful if it gets to a tax tribunal. It can also be a good thing to have in reserve if they try to launch a third inspection in the near future.
I have in the past succeeded in getting HMRC to close enquiries on these grounds. I've also encountered a situation last year where an HMRC inspector attempted to open a new case into my client without being aware that he had an inspection for the same tax just six months prior - so clearly HMRC sometimes make such a muddle of things that they don't realize they're retreading an investigation they've already covered.
I would dig my heels in on this and point out that a correction was already agreed. Point out that any further attempts to start the entire inspection over would amount to a fishing expedition and be an unreasonable expense to your client.
There might not be a way to conclude this without friction, but I guarantee that if you let this inspector back in, he will do his absolute hardest to increase the assessment. Otherwise he'll be unable to justify the use of his time to his supervisors.
HMRC don't just get to do things over endlessly until they find the answer they're looking for.
No, clients don't know the difference and even if you were to explain it to them they really wouldn't care.
That would imply that there's some conflict between their duties to the big four and their duties to small practices.
They aren't conflicted, they almost exclusively represent the big four and don't really give a damn about small practice. We don't throw money at them like the big four do.
As Duggimon said, you can't specify at the outset that they have to sell the shares back to you at a specified time.
What I believe you can do is have rules in the articles of association that require you to have right of first refusal if a shareholder wishes to sell their shares (i.e. you get first option to buy them) and rules over who they're allowed to sell the shares to. This should give you some scope to keep control of the entity once your EIS investors cash out.
As with the above, I would make sure he documents what he was researching when abroad, but assuming that he is carrying on genuine research I see no reason why these wouldn't be allowable.
There are other threads on here clarifying how to treat travel expenses if there's some holiday element to an otherwise business treat so it's worthwhile familiarizing yourself with what you would need to disallow. In general though I would take the attitude of claiming for it but documenting thoroughly the business purpose of the trip as it's liable to be queried by HMRC if they do an inspection.
They made such a cockup of MTD that they had to transfer a lot of other staff over to try and deal with the fallout of that. Brexit too.
All refunds are massively delayed at the moment - R&D in particular. You're probably looking at a few months to finally receive your refund at the moment.
I'm confident that as long as the OP keeps contemporary records and properly enforces the line that his record keeping would stand up to an HMRC on-site invigilation.
Very serious - liquids are the tricky part since you need to measure both the solid value using scales (e.g. how much coffee you spoon into the pot) and the seperate liquid quantities of any milk etc, which you have to use a measuring jug for.
I think you would be best off analyzing each transaction individually - to keep yourself right.
Start by setting up a log sheet in the kitchen to track who is taking biscuits or tea and coffee and when, this way you can properly disallow biscuits and coffee/tea consumed by clients rather than your own staff members (for liquids you'll probably need to use a pro-rata basis unless you want to introduce scales or some other more precise measurement system).
If you really want to cover yourself add an additional column to allow staff to log the purpose of their biscuit consumption (Are they merely consuming biscuits on a recreational basis or are they consuming them solely for business purposes?).
With that in place, I would set up four different nominal accounts on your ledger:
Using the log sheet you set up earlier, you can then split each of these individual categories into "Staff expenses" for when staff are eating biscuits or drinking tea/coffee within the office, "Business Entertainment Costs" for when they are consumed by clients (This should be added back) and "travel expenses" for situations where a staff member takes a biscuit for subsistence purposes while engaging in business travel.
This should ensure you properly account for all of these expenses in the appropriate category - hope it helps!