Quick fix for broken FTL hatch even if you have already done repair quest and still cannot travel to other system ( maybe your game crashed or you are using mods that caused this )

use console commands:

/admin

While pointing your mouse over broken FLT hatch
/entityeval object.smash()

delete item

/spawnitem hylotlfuelhatch ( you can edit command with race of your character - apex,human etc. )

place your new repaired fuel hatch

enjoy !