Ok, I took a look at it, eventhough your asset folder was missing some of the referenced assets, I could take a look.
From what I can see, the references that are problematic are the following:
batterie.mb
horloge.mb
microphone.mb
guitare.mb
etagere.mb
all the other references looked fine. Now guitare.mb itselfe contains a reference that I didn't have so I'm not sure about that file, but from what I could tell from the others, the problem pretty much fixed itself for those references by doing the following:
1) delete the reference cleanly
2) create the reference again
3) parent the reference under the corresponding locator
4) set rotation and translation to (0,0,0) and scale to (1,1,1)
now doing this for 5 references by hand is quite annoying, and I didn't find what exactly the problem was. So I'm not sure if those references will spontaneously corrupt again. So I wrote a short script that does these steps for you.
Just select the toplevel groups of the reference files that have a corrupted connection and run this script from a python tab in your scripteditor:
import maya.cmds as mc
sel = mc.ls(sl = True)
for s in sel:
par = mc.listRelatives(s, p = True)[0]
fn = mc.referenceQuery(s,f = True)
mc.file(fn, rr = True)
asOld = mc.ls(assemblies = True)
mc.file(fn, r = True)
asNew = mc.ls(assemblies = True)
refGroup = set(asNew).difference(asOld).pop()
mc.parent(refGroup, par)
refGroup = mc.listRelatives(par, c= True, pa = True, typ = 'transform' )[0]
mc.setAttr("{0}.s".format(refGroup), 1,1,1)
mc.setAttr("{0}.r".format(refGroup), 0,0,0)
mc.setAttr("{0}.t".format(refGroup), 0,0,0)
Now some things I would do to minimize the risk of this happening again:
1)Delete non-deformer history in your referenced files. They have a lot of construction history on them that isn't really useful at this stage and slows down your scene. <- I have a suspicion that this caused the corrupted links, all the objects with problems had polyChipoff nodes in their history, but that could just be a coincidence
2) If there is a reference in your referenced file, import that reference into the referenced file
3) make sure that the playback speed is 25 in all referenced files (this kept giving me warinings, but I don't think it was what caused the problem)
I hope it helps!