In Muhamamd Abduh I noted that Muhammad Abduh was reported to have issued a fatwa allowing prayer with shoes on, and himself to have prayed with his shoes on, and said that the explanation of this was unknown (pp. 101, 114). An explanation is now indicated, thanks to Thomas Eich, who drew my attention to M.J. Kister's article, "'Do not Assimilate Yourselves...' Lâ tashabbahû...," Jerusalem Studies in Arabic and Islam 12 (1989), pp. 321-353.
According to Kister, the general practice of removing shoes before prayer is a development that may be dated to as late as the seventh/thirteenth century (p. 346). There are numerous hadith on the issue of whether or not shoes should be removed for prayer, pointing both ways. In Kister's view, the original logic was the since the Jews of Arabia removed their shoes to pray, Muslims should not; this was part of a general trend towards encouraging differences in behavior between Muslims on the one hand and Jews and Christians, whose religions were understood to have been abrogated, on the other hand (pp. 336-40). The practice of wearing shoes for prayer later changed, however, as "a result of the significant changes in the social and material conditions of life," notably the building of elaborate mosques with floors covered with carpets (pp. 346-47), which had not existed in Arabia at the time of the Prophet. Shoes are not good for carpets. Kister's analysis is convincing.
Evidently, Muhammad Abduh was aware of the discussion that Kister has analyzed. There would then be two possible reasons for him to revert to the earlier practice of prayer wearing shoes. He might simply have decided that prayer wearing shoes was the practice of the Prophet and his immediate followers, but this is unlikely, since there are no other known examples of such a decision based purely on such grounds. Alternatively--and this is more in character--he might have decided that a practice of the Muslims that was at variance with the practices of Europe did not, in fact, have any real justification, and so could be abandoned.