Update/Patch an AGP-recorded genome assembly?

Question

[Felix Bemm]

I have a genome assembly stored in an AGP file with associated sequences. The AGP file was produced during an optical map driven scaffolding step. Additionally, I have a set of patches (wrongly compressed repeats, wrongly expanded repeats, wrong joins) that affect both the contigs and the scaffolds. How would one, in a traceable manner, update sequences and the AGP file to correct contigs and scaffolds? In an ideal case, the system reads a bed file with the annotated patches and applies them without involving a graphical user interface (for projects with hundreds of individual genome sequences). Ideas warmly welcome!