If the assessment is raised through normal UK trading, then HMRC can apply to the courts to wind up a UK limited company for an estimated assessment. However, it will usually only do this as a last resort.
Estimated assessments are normally issued only where VAT returns are missing. If there are missing returns, it would be recommended that the correct amount of VAT is calculated. If the true amount is less than the estimate, then the returns should be submitted to HMRC and a proposal to pay the outstanding VAT should be made to HMRC before winding up proceedings continue.
If the actual debt is larger than the estimate, it would be wise to calculate all other outstanding debts of the business and to check if the business is a "going concern". If the only creditor is the VAT man then it may be possible to arrange to pay off the debt in stages.
If the business debts are substantial then you should consider talking to an insolvency practitioner who would be the best person for advice. They will also be able to provide specific advice regarding the personal liability of the directors.
In order to comment on "EC regulation article 3" you would need to provide your adviser with further details, specifically which EC directive it belongs to, as there are numerous sections of EC legislation relating to VAT and other indirect taxes such as import duty and excise duty.