A 1-0 defeat at home to basement side Redbridge on Saturday coupled with a win for third from bottom Waltham Abbey at Heybridge Swifts confirmed Side's relegation three years after coming up as Essex Senior League runners-up in 2013.
After finishing one place above the drop zone last season the Essex club now need a summer reprieve from the FA in their annual shake-up of Non-League to stay up but an upbeat Flanagan has told officials at the Cricklefield Stadium that they will be back one way or the other.
In a statement on the Essex club's website, a spokesman said: "The chairman would like to apologise to the club's supporters but is realistic to admit that as the club is punching above its weight in a highly competitive league it was inevitable that one season relegation would happen.
Barkingside
"He is proud that the club gave a good account of themselves on and off the pitch during their Ryman stay. Relegation was probably more due to circumstances rather than the club not being good enough as the narrow margin of defeats this season have illustrated.
"Unless the most unlikeliest of reprieves happens the club will once again prepare themselves for Essex Senior League football with the aim of achieving promotion again."
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