What is the ruling on wiping over shoes that do not cover the anklebones, and what are the consequences for someone who did this for a period and then stopped?

It is permissible to wipe over boots worn over socks, because boots are like sandals, and it has been established that one may wipe over socks and sandals. If you wipe over your boots while they are over your socks and pray with them, your prayer is valid. However, if you remove them after wiping and before prayer, the preponderant opinion is that the ablution remains valid. As for wiping over boots without socks beneath them, if they do not cover the entire feet along with the ankles, then the ablution is invalid, and you must make up the prayers performed with that ablution.