Both Lowe's and The Home Depot offer window installation but don't mention anything about doing repair work to areas effected by water damage.
They offer you a credit option
If you want to get your window replaced but also have some of the boards that are damaged by water under the window's base, including part of the wallboard caused by a leaky window air conditioner unit, you may be able to get a general contractor over to assess the full extent of repairs needed, but if you call Lowe's or The Home Depot they will come by at a specified appointment time and date to give you a free estimate.
If the damage is beyond the scope of just removing and replacing a window it is up to the individual discretion of the man who comes over to look at it.
The man may say, "There is some water damage to the wall board and support studs inside the wall that will require additional labor and materials. If you are willing to pay such and such amount over the basic installation cost I am willing to consider doing the work for you but it is not what I normally do." or they might say, "Sorry ma'am, this window is too far gone. The damage to the wood and wall tile will cost a lot more. You can apply for a credit loan if you want and maybe we can find a contractor for you." or they might just say, "No problem, the total will be under a thousand dollars including replacing the few damaged wall studs and the framework of the window as well as the drywall." That is what I am hoping for, but that may not happen. We have tried to get one window replaced and it was done but the general contractor who did the work bid over 3 thousand to do the work and it would take a long time for us to save for the smaller window that is in need of replacement so I can expect that particular contractor might do the work but charge nearly 3 thousand to do so.
It would be nice to be rich. Meantime, if you think you are getting an estimate to just replace a window, think more along the lines of, what else might be in need of repair around the window.
This includes the window frame, the window facing, the studs that support the window to the floor base board and the inner wall drywall and the base trim and corner molding and then there is the exterior tile removal, and replacement and subsequent patching, painting and drywall tape and bedding, the cost of lumber, drywall and siding. All this because the AC window unit sweated and resulted in the initial rot of the window sill that was never replaced.
If I had removed that AC unit from that window 10 years ago, replaced the window sill and then had a man come by and just replace the window it would have been under 500 dollars but hind sight is 20/20 and I now realize the price I will pay for putting things off until never.
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