Dear has the useful ability to lock the system while a stock-take is in process to prevent sales orders being generated which would make the count inaccurate.
We have a lot of stock items and it's not feasible to do a complete stock-take in one go. However, when uploading a stock-take CSV file any uncounted items are set as zero stock.
To get round this we did a partial stock-take and then for all the items not counted we just entered the 'Quantity on hand' amount as shown in the exported CSV file from Dear so that all the uncounted items retained the same value of stock.
Then we manually keep a record of which stock was counted and repeat with the uncounted stock when we have time to complete the stock-take.
This does require a bit of spreadsheet fiddling but can be easily solved with a bit of sorting and a VLOOKUP to fill in the uncounted items.