Flask upgrades

Why is it whenever I go to upgrade a flask, that health/mana points go down significantly?

Not sure exactly what you mean, but some flask mods increase the amount of regeneration.

There are mods that reduce amount recovered but give other benefits such as instant recovery

What i mean is, whenever I upgrade a normal flask to a magical, if it started out as +1000 to health, after upgrading, now it gets lowered to say, +600. Is that normal? Should I not worry so much about the total amount and just look at what magical attributes it just got?

It sounds like what you are doing is upgrading 3 magic flask to 1 higher level flask via vendor recipe?

There's 2 factors, the change of the base flask and then change to any mods rolled on the flask.

Here is a list of the base flasks.

https://www.poewiki.net/wiki/Flask

You can see with the base properties for life flasks, in general, the flasks get more life recovery as you upgrade them. However there are some exceptions. Sanctified flask has less overall recovery than Hallowed flask. You will see the flasks also have a duration. Sanctified also has a shorter duration. The upside of this, is that the recovery rate is much quicker. Depending on your build, this may or may not be desirable. You will notice a similar thing with Divine vs Eternal life flask, even though the vendor recipe doesn't upgrade to those levels. So in general upgrading will give you better flasks, but there are situations where you may not want to. Sometimes lower recovery rate might actually be preferred. Though many builds will want the recovery to be as quick as possible.

The next thing is the mods. As stated in above comments, some mods increase or decrease the amount of recovery, as well as other properties of the flask. For example, mods that make recovery instant have reduced amount recovered. So if your upgraded flask gets one of these mods, it may have less overall recovery, even if the base was increased. Same thing if your lower base flasks had mods that increase total recovery and they where change when upgrading. You may end up with less overall recovery on the higher base.

You can roll the mods on the base of the upgraded flask with alterations and augments if you want a specific mod.

Here's a list of the possible mods for life flasks.

https://www.craftofexile.com/?b=60&ob=both&v=d&a=x&l=a&lg=17&bp=y&as=1&hb=0&bld={}&im={}&ggt=|&ccp={}&gvc={%22limit%22:88}

On life flasks, the prefix will modify the amount of recovery/ duration etc. The suffix will have a range of other properties, as you can see on the list. Notice also the level of the flask, like on items, will determine which mods can roll.

Wow, this is a lot to understand for just life and mana flasks. I think I need to find an easier game....Lol

Its not all that complicated. As you play, you'll find newer, better potions. Typically, the higher the initial level requirement the more health it will give you.

Beyond that....the mods you might roll on them are self explanatory, they just require reading.

Every other game is going to be at least that complicated when it comes to items. Higher level = better (in general), mods require reading.

You don't need to know all that. Flasks are an after thought for most new players. If your already learning it your probably starting to understand the game mechanics. As above reading is pretty important in this game. If you doing that and information is not there, it's probably available on the wiki, third party or as you are doing, asking on the forum.