you for reaching out on the community and telling us about your issue. I do apologize this is happening to you. Is there any sort of similarities for this happening? Something like a specific time frame or is it at random?
There's 2 ways to go about getting the transactions back to a reconciled state. The first being loading a backup of your file that should have all the transactions back in their previous state. If the back up is from a couple of days you would likely need to put some newer ones back in again. If you're unsure how to do this I've linked an article above that will guide you on loading a backup.The second method would be if the accounts still have the correct balances is for us to quickly change those transactions that aren't marked reconciled anymore.
Click on the column header labeled CLR
Next click on the first transaction that needs to be cleared. They should still be in a date order which helps find which ones shouldn't be reconciled just yet. Find the first transaction that should be reconciled and click on it. Next find the last transaction that should be reconciled on your list. Hold SHIFT on your keyboard and click on the last transaction. This should highlight everything inbetween the first and last transaction. From here right click anywhere in the highlighted area and select reconcile status-> Reconciled. This will put them back in a reconciled state.
This should help you out with getting the account sorted out again. Please let us know how it goes and the other details when you get a chance.