Yes, when you input the relevant information. If you select the Flat Rate Scheme in your VAT settings, the tool will assume that no VAT can be reclaimed on any expense. To reclaim VAT on certain capital expenditure over £2000, you need to change the settings on that particular transaction by switching on the “Recoverable Capital Good” toggle in the VAT section of that transaction, either in transaction details or the bookkeeping section.
You should then select the VAT amount or rate you paid on that purchase. Changing these settings will ensure that the reclaiming of VAT on this transaction is now included in your VAT calculation.