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It's not so much a question of the time of year to re-pot but conditions that warrant a re-potting. Re-pot if your lobelia is root bound, outgrows its pot or when the water doesn't quickly drain. Trim back the roots and the top of a plant and repot in the same container (or the next larger size) with some fresh potting soil.

For more information on growing lobelia, please visit the following link:
https://www.gardeningknowhow.com/ornamental/flowers/lobelia/lobelia.htm

Here is a link to refresh you on the care requirements.

https://www.gardeningknowhow.com/ornamental/flowers/cardinal-flower/growing-cardinal-flowers.htm

It is probably either woodchucks, rabbits or deer. For more information on how to keep these animals out of your garden, please visit the following links:

https://www.gardeningknowhow.com/plant-problems/pests/animals/keep-rabbits-out-of-gardens.htm
https://www.gardeningknowhow.com/plant-problems/pests/deer/deer-repellents.htm
http://pss.uvm.edu/ppp/articles/woodchucks.html

There are a number of critters that can dine on garden plants.
Rodents, Squirrels, Chipmunks, Rabbits, to name a few.
Here are some articles that may help you.

https://www.gardeningknowhow.com/plant-problems/pests/animals/

Lobelia does have naturally slow-growing seedlings, so don't worry if they are smaller than your other seedlings planted at the same time. Lobelia seedlings are especially vulnerable to damping off, explained in the following article:

https://www.gardeningknowhow.com/garden-how-to/seeds/what-is-damping-off.htm

To prevent damping off, make sure the soil doesn't stay too wet- it can be just slightly damp while the seedlings are small. Then, when the plants have grown bigger, you can water them normally. You can also keep the tray in the sun, unless it is very hot.