Being as Bolton Wanderers are not going to play their final two matches of the season, the simple way of dealing with this situation may be to award 3-0 wins to Brentford and Nottingham Forest.
As the Trotters are unable to complete the season, they might as well go straight into liquidation, with all the other clubs below them moving up one slot. This would mean for example in the third tier, the top 3 teams are promoted automatically with 4th to 7th being in the play offs. The basement division could have the first 4 teams promoted automatically with 5th to 8th in the play offs, This would work its way down through the pyramid system and would not affect the relegation slots. A brand new incarnation of Bolton FC 2019 or something like that could be formed and apply as a new member of the FA, or alternatively, the town of Bolton could be absent from league football for a few years and stage a comeback with a new side similar to Accrington Stanley, who never resigned membership of the FA.
There is a precedent in Scotland when in 2002, the original incarnation of Airdrieonians went into liquidation after the final game of the season, with all the other sides all moving up one slot. It is noted that this was in the days when it was a simple 2 up 2 down with no play offs. Mentioning of precedents that started in Scottish football (and on a sideways move from Bolton Wanderers), Meadowbank Thistle relocated from Edinburgh to the New Town of Livingston back in 1995 and changed name accordingly. Eight years later and with a lot of controversy, the original incarnation of Wimbledon relocated to Milton Keynes and changed their name accordingly.