Take a look at the HMRC manual pages on ER here
and at some independent commentary here
The fact that the company no longer owns the flat is a good thing. Provided the company (you) was not engaged in activities ancillary to the main business for more than 20% of the total time spent engaged in company activity or the income from non-trading activities did not contribute significantly to the company's bot***** *****ne, claiming ER successfully should not be a problem.
Once concern is that you have a sizeable cash balance in the company which HMRC may see as being excessive compared to what is needed to run the company and some of which may be the profit made from the sale of the flat. If you can take some of that as dividend, it will help, but obviously you want to avoid incurring a higher rate personal tax liability.
You may or may not be aware that there is now a £25,000 limit on cash being distributed as capital (as opposed to dividend) where an informal liquidation of the company is planned. You can read about that here
. In order to withdraw more than £25,000 as capital, a formal liquidation process has to be followed and a liquidator appointed. This can be expensive, though the proliferation of such services available through the internet has pushed prices down significantly.
I hope this helps but let me know if you have any further questions.