Join Date: Nov 2013
Location: Millgrove, ON, Canada
If you leave the battery connected, not an issue, just remember on a lot of bikes there is a small parasitic draw to keep the clock going and your trip odometers maintained. So, it will discharge the battery over time.
A fully charged battery is 12.7-12.8 volts, half charge is 12.3-12.4. If a battery is discharged to below half a half dozen times or so, sulphation sets in... of course, the longer that sits in that condition it isn't good.
There are debates whether one should leave a Battery Tender hooked up ALL the time, I prefer to unplug for a couple of weeks, but I have left it plugged in all the time also with no ill effects. I imagine the only concern is if the Tender malfunctions in some way, but very reliable so I don't worry about that too much.
The Battery Tender Jr. will have a tough time having enough ooomph to recharge a dead battery, so I'd only use that on a decently charged battery.
Properly maintained, a AGM battery should last 5 years unless it's being cooked constantly in a hot climate. Heat is the enemy.
Along the lines of PTRider's comments, you can disconnect and fully charge a battery, put it into freezing cold storage with nothing connected and it will stay charged for a fair long time. Check with a voltmeter once a month and you should be good to go.