If you are okay with the above all whilst knowing that this method does NOT work for everyone then you can proceed to the step-by-step guide, but please do so at your own risk as it may not work at all.
Update 11th May 2012 -
1. Please note that completing the initial merge does NOT mean that your habitarium will be unlocked. It is just a foot in the door, or preparation if you like. What you do AFTER the merging will *hopefully* unlock it.
2. Rescue(alternate) Habi's sometimes get stuck when trying to unlock a main habitarium, but they are not locked out. Just load it up again! You may have to refresh the Habitarium a few times to unstick it.
3. Do not delete EVERYTHING from your bag. Save a few pages of eggs. This will help you to level up quicker if you end up having to reset. Get rid of the decoration and structures first as you can be gifted these items when you regain access to your habitarium.
• Step 1 - First you need to LOGOUT OF NEOPETS, then open 2 tabs in one browser. (You can use any browser that allows tabs such as Firefox or Chrome)
• Step 2 - Go to neopets.com on each tab, you should navigate to the login page on each tab by clicking on "Login to Neopets" on the top right of the page.

• Step 3 - In One tab, login to an alternate account, and start the Habitarium game. If the alternate account does not already have a habitarium you must first go through the tutorial before touching the other tab. IMPORTANT: If you are attempting this using a side.. once you have finished the tutorial do not continue to try level the side account's Habitarium up as that is against the rules! If a friend/family is helping then of course it is allowed to level it although not required in this guide.
• Step 4 - In the Other tab, login to your Main, and try to load Habitarium (it will not load yet - this is normal). Keep BOTH tab's open at all times.
• Step 5 - Now switch to the tab with the alternate habitarium and open the inventory bag. If you have been successful with this method so far then you should see items which are from your main accounts bag. Now its beginning to merge!

• Step 6 - Go through the bag and begin to delete items. (IF you have a MPET on your board you SHOULD delete ALL but 9 eggs - one of each type of each species so a Larnikin/Pinchit and Mootix Soldier/Worker/Nester = a total of 9 eggs! Unsure what a Mpet is? You can learn about them here) Whilst doing this you can occassionally refresh the tab with your main account's Habitarium but do NOT refresh the tab with the alternate accounts Habitarium as this will mess the process up. Some people have only needed to delete a few items whereas others have had to delete everything. It's up to you how far you are willing to go!
Eventually the two games will merge, you will know this is happening as odd behaviour can be observed. For example if you are a victim of the gem-lockout you might see gem's appear to pop up even though that account is not level 50, or you might see notices in the top left appear stating that your neofriends have repaired things for you. Another sign of merging is your main account's neofriend list appearing at the bottom of your alternate account's habitarium.
Another option you can attempt which can boost the merge is to purchase an item from the shop on the alternate habitarium, it is best to choose a cheap option such as a Cornmeal. Once you purchase this you may see the level of the alternate habitarium change to 50 if it hasn't already and when checking your resource count they should be your main habitarium's resources now rather than the alternates. REMEMBER to delete the item you buy after!

As you are going through this, you can try to refresh the Main tab again to see if it loads. You should make a habit of refreshing the main tab's habitarium on occassion.
• Step 7 - Some people may find their habitarium has unlocked already but this step is still provided as an extra action to take which could unlock your habitarium if you have been unsuccessful up until now. So, once ALL items have been deleted: On the alternate habitarium you should have a storage/building which was built during the tutorial (or if you are using a friends account for the alternate Habitarium then use one of their buildings!) Move the building around the alternate gameboard and continue to refresh your main Habitarium tab whilst doing this.
Step 7 UPDATE 22/10/2011 - I personally have been locked out 3 times so far from a Gem Lockout (too many gems on the board). I found doing the following fixed it every time:
• Take the storage/building on the alternate Habitarium which was built and place it on the exact square where an identical building would be on your main Habitarium. So for example if you know that on your main Habitarium you had a storage in the top right corner, then on the alternate Habitarium you should drag a storage onto that same square on the alternate Habitarium (It must be the same building, so if using a nest you must drag it on a square that has a nest on your main), it is VERY important that you do not do the next step for at least one harvest cycle (generally 30-45 seconds), I personally would recommend waiting 2 minutes before attempting the next step. If you cannot remember where things were on your main then you can attempt to ask a neofriend to view your Habitarium through NF's and tell you where things were or take a screenshot.
(Attempt the following below whilst refreshing your Habitarium now and again throughout)
• On the alternate Habitarium move the building which you placed one square in any direction, now wait 2 minutes before moving on to the next step.
• On the alternate Habitarium move the building which you just moved, BACK to the square it was on before, again wait 2 minutes before moving on to the next step.
• Drag the building into your bag
What we are trying to do here is get the alternate Habitarium's building/storage to merge with the mains so what you're actually doing is first off merging the building and then dragging it into the bag (if it has worked then that would mean you have dragged a storage from your main Habitarium into the bag) which would be enough to unlock it!
If this doesn't work immediately for you then you can expand on this by moving the building between several squares that have the same building on your main. So if you're choosing a Storage, place it on each tile where there is a storage on your main (even try move it back and forth between those select tiles) and THEN put the storage in your bag. You could also attempt this using a House or a couple different buildings at one time. {Please Neomail Sralini if this particular step works for you as I am curious how well this will work for others based on how fast it worked for me each time.}
Please bare in mind that this might not work the first time around, you may completely empty your bag and no signs of merging has occurred. In this case you should log out both tabs and try the process again, by doing this you might then notice that items appeared in your bag that were not there before so you should try to delete these and repeat the process a few times if necessary.
It is entirely up to you to stop when you feel uncomfortable deleting any more items, in which case you'll have to wait for the general fix.
So far Gem-Lockouts and Watch-it-die Lockouts have been corrected by this method, but it does not work for all cases.