Plumbing – Toilet bowl level drops after flushing

The only possible reason for the water loss, and that if you're not getting any noticeable leakage, is improper venting, as described here.

There is another reason why it seems that improper venting is the cause - you noticed that the water level was getting lower over a year period. It could be that over that year your plumbing venting clogged slowly & steadily.

Also, contrary to what is said in the link above (that in a case of improper venting you need to call a plumber), I think that if you've noticed the change over a long period, this is also reversible (bird nesting or something similar).

If the problem was very low but steady water level, then it could be a problem that require a plumber's work.

If you had "the sewage line get backed up" all along and didn't do anything to fix it (replacing the water line doesn't) then the sewage line will only get worse.

As for your tub (I think you want me to guess you shower in the tub instead of having both a tub and a separate shower), it probably connects to the sewage line after the clog that affects your toilet.