Replacing toilet anchor bolts is not hard if the toilet is already removed. If you have to take it up for another reason then it makes sense to replace the anchor bolts. If the toilet is older, you likely ruined the anchor bolts getting the nuts loose.
Problems With Toilet Anchor Bolts
Toilet anchor bolts have a tendancy to corrode over time. If the toilet has been in place for a number of years, the nuts on the anchor bolts will be frozen and difficult to remove.
The other problem is the design of most toilet flanges. The 'tee' bolts as they are sometimes called need to have upward pressure on them when the nuts are removed. The 'tee' portion has to stay up inside of a recess in the flange to keep it from spinning. This is much harder to do than it sounds. Some plumbers will install a lock nut on the bolt to hold it in place and keep it from spinning.
Removing Toilet Anchor Bolts
To remove the anchor bolts, you need to remove the toilet. This sounds contradictory, but it is not. To remove the toilet, you need to remove the nuts on the tee bolts. See the article 'How To Remove a Toilet' for instructions on taking up a toilet.
Once the toilet is removed, the anchor bolts will slide in a slot on the flanges to a spot where they can be removed. If the nuts are frozen or the tee bolts are badly corroded, you may have to use a hack saw and cut them off, this of course ruins the anchor bolts.
Purchasing Toilet Anchor Bolts
Most toilet flanges that have been installed in recent decades use a 'Tee' style anchor bolt. It is a threaded bolt, that has a flat oval shaped end. The oval shaped end fits inside a slot on the toilet flange. The flat portion pulls against the flange and hold the toilet to the floor when the nut is tightened.
Some older toilet installation will have a lag bolt that screws into the floor. This type is troublesome, since there is a tendency for the wood in the floor to rot out around the anchor bolt.
Buy and extra set of nuts and washers. Install a nut and washer on the flange before you reset the toilet. This holds the bolts in place and eliminates the stripping problem.
At the supply store they may tell you that you don't need extra nuts. As mentioned above, when everything is new this is true. If you are certain you won't have to work on this particular toilet again, you can skip the extra nuts. I have found that having the tee bolts secure makes setting the toilet much easier. We are talking about less than a dollar for two extra nuts and washers.
Installing New Anchor Bolts
When you install the anchor bolts, use a set of nuts and washers to lock the bolt to the flange before you try and install the toilet. The bolts should be placed at 'Three' and 'Nine' o'clock when you are facing the toilet. Locking the bolts in will make the installation of the toilet and tightening of the nuts much easier.
The second set of nuts will go on the toilet. after it is installed. A trick is to use a couple of straws on the bolts to help guide the toilet when you are setting it. See the article 'How To Install a Toilet' for full instructions.
After the toilet is installed, the bolts may need to be cut down to the correct height. Use a hack saw for this chore.