Can I do freehand embroidery using this machine?

Not sure what your machine is capable of but many machines have a function for freehand darning/embroidery - maybe that would fix the hole...

Free Motion Embroider Drawing With Your Sewing Machine

How To Do Free Hand Machine Embroidery

Free Motion Machine Embroidery Part 1 with Christopher Nejman

If you can drop the feed dogs (or have a plate to cover the feed dogs), the machine has a zig-zag stitch, and you have a darning foot or free motion foot, you can do free motion quilting, hand manipulated embroidery (monograms), and applique on a basic sewing machine. It will take some testing and quite a bit of practice. You can also use an embroidery foot to monogram and applique. You will want to sink the needle into the fabric at every corner and frequently when creating curves so you can move the fabric.

Search the internet for instructions & tutorials on how to set up your machine and the best way to accomplish what you want.

How to Monogram with Basic Sewing Machine

How to Use Monogramming Foot

Machine Applique Tutorial

Machine Applique Sewing

some machines have an option to lower them for freehand darning or embroidery.

A manual feed is used primarily in freehand embroidery, quilting, and shoe repair. With manual feed, the stitch length and direction is controlled entirely by the motion of the material being sewn. Frequently some form of hoop or stabilizing material is used with fabric to keep the material under proper tension and aid in moving it around. Most household machines can be set for manual feed by disengaging the drop feed dogs. Most industrial machines can not be used for manual feed without actually removing the feed dogs.

here is a link for a manual, the information should be in the manual
http://www.sewingpartsonline.com/instruction-book-janome-and-newhome-9000.aspx

How about taking off your presser foot and put your work in an embroidery hoop. then guide it around by hand? That is what I do for freehand.

I do not believe the bobbin thread is the reason for the problem.

Refer to your manual for maintenance, especially cleaning the bobbin area.

When you replace the bobbin case be sure the needle is in it's highest position and this will also set the shuttle in position to properly accept the case.

If the problem continues, then machine will need to go into the shop. If the timing needs to be adjusted, this is best done by a Bernina tech.

Won't sew can mean more than one thing - the machine has no power or is seized up; the needle is not going up and down; the needle and bobbin are not forming a stitch.

When the feed dogs are down, you move the fabric by hand.

The presser foot has to be down to stitch.

If you wound a bobbin before you starting the sewing, did you disengage the bobbin winding feature(s)?

I hate to sound dismissive but: read the manual. Duh. It is not as written above: drop dog........
The feed dog is the toothed pieces in the sewing machine deck, under the needle, which move the material away from you when you push the operating pedal.
Dropping the dog - ie making it inoperative - (see manual for how to on your machine) means the material has to be propelled by hand under the needle. This is especially good for freehand machine embroidery as it means you can move the material in any direction whilst sewing.
It can be easier to freehand embroider if your material is fixed in to an embroidery hoop to hold it flat while you work.