You will find that a lot of shops swear by bottled bacteria, the problem is that not many of them actually work.
I have googled that medication and found it treats against protozoan parasites such as whitespot (ich) and velvet. Does the pack say that it damages the filter bacteria or was that just what the chap at MA said? If it does say that, there are lots of other meds on the market which do not damage your filter bacteria.
I know you have just spent your money buying it, but you could try eSHa Exit, waterlife's protozin, King British WS3, or any other whitespot medication which will also kill other protozoan parasites. The problem is that these parasites have a stage in their life cycle where they encyst and can't be killed so if you put more fish in the tank they'll become infected. Personally, I would put the endlers back and try to find one of the other meds.
Whitespot (ich) and velvet (oodinium) have a three stage life cycle, though I'm not sure about trichodina or Chilodonella.
The three stage lifecycle is: the first stage is on the fish where it feeds off the fish's skin. It has a coating so meds can't get at it. The second stage is where it comes off the fish and rests on the tank bottom in a sort of cyst and multiplies. Again, because of the cyst the med can't get at it. The third stage is where the cyst releases 'baby' parasites which are free swimming and they swim off to infect a fish. This third stage is the only one where it can be killed. If your endlers have either of these diseases, there will be parasites in all three stages in the tank which is why the whole tank must be treated, following the med instructions to the letter as there must be some med in the water when the very last bug reaches the free swimming stage.
This is why I suggest getting a med that will not harm your filter bacteria. I have used both protozin and King British WS3 with no effect on my filter.