So far as I know doing visa-runs from Indonesia is ok - but more time-consuming and expensive than other countries due to the lack of land borders. When I was in Bali some of the cheapest flights were to Kuching, which was a good opportunity to take-in Borneo.
Depending on timescales, etc, there's a chance it might be cost effective for you to get a second UK passport (there are various grounds for doing this - try Googling) so that you can keep using your first passport whilst waiting for you visa.
Anthony
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