Yes, just delete it. My personal experience with Aloha (about 7 yrs now) has been the trans log corruption happens less and less as the versions continue, but when it does happen with newer versions, the chances of fixing in have dimished.
I guess that means when it does when it DOES happen, it's usually really messed up. Most clients we have just say screw it, they'll live without the data, they aren't interested in spending money on having it fixed.
If the system has been down for a few days, you might have to change the date of business and refresh after deleting the trans log in data. Otherwise, it may just run a few blank end of days to catch (not really a big deal).