I don't think you told us all the details
I wanted to export the catalog and suddenly all my photos are found in the root directory of my file .lrcat,
We know what you wanted to do, but exactly what did you do? Please explain in detail the steps you followed, using Lightroom names for the commands/function when possible.
All photos were properly stored in the catalog.
Also, photos are not stored in the catalog, and they are not stored in your .lrcat file, they are always stored on your hard disk, wherever you put them or wherever you instructed Lightroom to put them.
The link below is to a video tutorial that will provide a very good understanding about how the Lightroom Catalog file functions. Having a look at it will be very worth while.
If the photos are actually moved on your hard-disk due to whatever you did, then No, you cannot “remap to their original folders”. The LR import function just remembers where the photos were when you imported them. If you did something else that moved them all somewhere else then LR will see that they are missing.
I suppose one way to have done what you seem to be describing is to create a brand new catalog, do an Import into it using the Move option, instead of the Add option, and specify a common folder to put the photos in. This would remove the photos from the original location and put them in a single subfolder. If you opened your original LR catalog then they’d all be missing since their location has changed.
In fact, i'm not an expert as you can see. I'm beginner with LR and i did something with my catalog that i don't understand, that's why i can't tell you all the details anymore. What i can say is, before i had a catalog with a good organisation, all my photos were well organized, with synchronisation between LR and my HDD.
But from the time I made this export all my photos were moved into a single directory (44 500 files :-s). I think the only solution is to manually search the files for each directories ...
When you export from Lightroom, nothing happens to your original images. They are not moved. New copies of those images are created in what ever file format you choose, and those copies are saved to a new folder or to a location of your choosing. Did you actually use the "Export" function in Lightroom? If you did, do you know how to post a screenshot showing us what your export settings were?
In addition to what JimHess said, are you sure the original photos (not the exported photos) are no longer in their original folders?
Yes i'm sure that the original photos are not in their orignal folders. I think i made a new catalog and import files with moving options as ssprengel said ...