Diamond significantly cracked after being cleaned, looks very different compared to diamond given to jeweler. Any advice?

My wife recently went into our local jeweler with whom we recently had her engagement ring custom made (and who are currently working on making repairs to said engagement ring). She also brought in a natural diamond that the jeweler offered to clean for free. The diamond was top of the line in all categories except for cut and had one small fracture on the side. The jeweler had the stone for 15 minutes, which was significantly longer than they’ve taken to polish other jewelry we’ve taken in for cleanings.

When they brought the stone back out, my wife noticed that it looked significantly different to the stone she came in with and was highly included and fractured. The jeweler showed it to her under a microscope and told her it was fracture filled and that he’d only cleaned it with a toothbrush. My wife raised concern that it didn’t look like her diamond, but the jeweler insisted it was the same.

We’d brought the stone into a different store back in July for a cleaning, also viewing it under a microscope then. The stone at that time was confirmed to be the same high quality and showed the single fracture that it had since purchase.

I know switching stones is highly unusual, and this local place has a strong reputation and 50+ years of experience in the area. Does anyone have any opinions on what might have happened and what we could potentially do? We plan to take the ring back to the other store to confirm whether it’s the same stone. Unfortunately, we don’t have the GIA documents as they were lost quite a while ago.

TL;DR: wife brought in a diamond to a local store for a cleaning and what they brought back was significantly fractured, included, and looked nothing like what we saw under a microscope previously when cleaned.