The bonuses on equipment shouldn't be removed unless you un-equip the item or it gets broken (in which case repairing the item should restore the bonus). If an equipment slot is darkened, like the shield slot if you equip a two handed weapon, you will not get any associated bonuses.
If you un-equip and then re-equip the item, do your stats change appropriately?
Are you sure you are not seeing another type of bonus (from food, potion or spell) wear off?Food effects link
For a description of how mana and health are calculated, see either of the following topics.differences between classes
(minor spoilers)Early Starter Tips (NON-Spoiler Version)
(contains much of the information in the above topic)
If you wait long enough for any food/potion/spell effects to wear off and remove all equipment with stat bonuses (or make sure to take them into account), then the sum of
strength + agility + intelligence + constitution + any unassigned stat points
should be equal to
40 + 5*(Character Level) + [color:"#3A495A"](+5 or -5 bonus from Shrine of Good and Evil)[/color] + [color:"#3A495A"](+5 or +10 stat bonus from Wishing Well, if that was the wish you made)[/color] - [color:"#3A495A"](1 to 4 stolen by vampire in the dark cave if you saved the boy)[/color] + [color:"#3A495A"](+20 from the agility bonus of Finnigan's magic lockpick)[/color]
(spoilers; highlight the text to read)
The terms in spoiler text you will have only encountered if you have explored the far east or north east of Rivertown, or been to Verdistis.