First of all, BCAAs are branched-chain amino acids, and amino acids are the building blocks for protein. Your body can get amino acids from protein sources by catabolism just fine. Eat good protein sources, eat varied and supplement only as needed. Paying a premium for things that are needlessly complex (such as whey isolate instead of simple concentrate) rarely makes sense.
1.) Can the use of Whey Protein supplements adversely affect/increase blood cholesterol levels? Is this a known fact?
Searching for "whey protein cholesterol" immediately yielded a study observing the exact opposite: http://www.ncbi.nlm.nih.gov/pubmed/20377924. Supplementation with whey protein in this case yielded a notable decrease in total cholesterol and LDL cholesterol (the "bad one") compared to non-supplement and casein supplement control groups.
One study isn't conclusive when it comes to complex nutritional issues but at least it should set off your BS alarm when a trainer claims whey protein is going to affect your blood lipid levels in a bad way.
2.) Could the use of BCAA instead help with muscle tissue growth and repair without affecting blood cholesterol levels adversely?
Most of what I find seems to study BCAA supplementation effects on groups with specific pathologies, where increases in blood lipid levels may in fact be required. I'm not finding resources suggesting BCAA supplementation would adversely affect cholesterol levels for healthy people.
I'm finding some claims for reductions of serum levels of cholesterol by intake of taurine, arginine and carnitine, but none of those are BCAAs (and taurine is not strictly an amino acid in the dietary sense). I'd be critical of this anyway.
3.) For how long would one usually take BCAA's and would there be any serious adverse health effects in the longterm from taking them?
Amino acid and protein supplements don't require cycling or tapering. They simply provide some extra nutrients which you'll already find in food in similar levels. That's it. There's no reason to believe there are any long-term problems with taking them if they don't displace an otherwise healthy diet. Claims that a high-protein diet would be harmful to the kidneys are also total bunk based on the protein restriction prescribed to people who already have kidney dysfunction.
4.) Can the use of Creatine help with energy levels? Like helping you kick start your gym sessions with a little boost ( and thus overcoming the fatigue from a day's work )?
Maybe a little. Creatine will assist in ATP (adenosine triphosphate) turnover from ADP (adenosine diphosphate). This could help with recovery between sets, maybe a some extra strength available before a muscle fatigues. I don't think it's going to do much for your general energy levels.
If anything would help when you feel low on energy during workouts, it would be carbohydrates. These provide the glucose needed by muscles for force production. Protein is required for building muscle and can also provide energy, but when it comes to energy levels during a workout session you'll find glucose levels have a much more profound effect, and carbs are simply the easiest and most direct source.
I leave you with some further notes. The relation between dietary cholesterol and blood cholesterol levels has come under scrutiny. Dietary cholesterol used to be thought of as the primary driver for blood levels for a long time but that stance is being re-examined (and outright rejected in some cases). So it's possible that leaving out the eggs isn't really helping you.
There's been a lot of flipping on the cholesterol issue with new surprises springing up every so often. Cholesterol used to be bad. Then it was found there's HDL and LDL with the latter requiring reduction and the former actually needing to be higher for some folks. Meanwhile the idea that dietary fat is a big problem came under scrutiny. Then it was said saturated fats were the problem while unsaturated fats were actually beneficial. The blame for the obesity epidemic shifted towards carbohydrates. But only refined carbohydrates. Then red meat was discovered to give you bowel cancer. Must be the saturated fat. Oh wait, no, saturated fat actually isn't the problem, we're thinking it must be the carnitine now.
And then there's controversy over statins regarding whether they're actually needed at all, if their benefits outweigh the risks and if the cholesterol scare isn't even an artificial problem in the first place.
You see where I'm getting at? Each piece of the puzzle brings 5 other pieces out of alignment. Doctors can't be expected to be completely up-to-date with all the latest nutritional studies, and even if they are they can only operate on the current state of knowledge. Which is also what doctors did 20 years ago when they told you to eat less fat, and a couple centuries ago when mercury was the magic cure-all. So with that in mind, how do you expect a trainer to know much better? With all due respect to some of the good trainers out there, most PT's don't know sh*t.
All I can say is, learn as much as you can from the information out there, be skeptic of everything (broscience and actual science alike) and find out what works for you. Long story short, protein supplements probably won't do much for your cholesterol level, creatine is useful but no miracle supplement (it's actually quite subtle) and some carbs would help you with that workout energy. Don't panic if increasing carbs leads to some quick weight gain, that'd be water retention from the glucose/glycogen.